List of supported software¶
Note
This page contains a lot of information, it may take a while to load.
EasyBuild supports 3085 different software packages (incl. toolchains, bundles):
a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z
3¶
3to2¶
lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x.
homepage: https://pypi.python.org/pypi/3to2
version | versionsuffix | toolchain |
---|---|---|
1.1.1 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
1.1.1 |
-Python-2.7.13 |
intel/2017a |
4¶
4ti2¶
A software package for algebraic, geometric and combinatorial problems on linear spaces
homepage: https://4ti2.github.io/
version | toolchain |
---|---|
1.6.9 |
GCC/8.2.0-2.31.1 , intel/2018b |
A¶
ABAQUS - ABINIT - ABRA2 - ABRicate - Abseil - abTEM - ABySS - ack - ACT - ACTC - ada - AdapterRemoval - ADDA - ADF - ADIOS - adjustText - ADMIXTURE - ADOL-C - Advisor - AFNI - AGAT - AGeNT - AGFusion - aiohttp - ALADIN - Albacore - Albumentations - alevin-fry - ALFA - Alfred - alleleCount - Allinea - ALLPATHS-LG - almosthere - Alpha - AlphaFold - ALPS - alsa-lib - AMAPVox - Amara - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMD-uProf - AMOS - AMPHORA2 - AMPL-MP - amplimap - AMPtk - AmrPlusPlus - AMS - Anaconda2 - Anaconda3 - aNCI - andi - ANGEL - angsd - ANIcalculator - anndata - Annif - Annocript - annovar - ANSYS - ANSYS_CFD - ant - antiSMASH - ANTLR - ANTs - anvio - any2fasta - AOCC - AOMP - APBS - apex - APR - APR-util - AptaSUITE - ARAGORN - Arb - Arcade-Learning-Environment - arcasHLA - ARCH - Archive-Zip - ArchR - archspec - ARGoS - argtable - aria2 - Arlequin - Armadillo - arosics - ARPACK++ - arpack-ng - ArrayFire - Arriba - Arrow - arrow-R - ART - artic-ncov2019 - ARTS - ArviZ - ARWEN - ASAP - ASAP3 - ASE - ASHS - Aspera-CLI - Aspera-Connect - assimp - Assimulo - ASTRID - astro-tulips - astropy - at-spi2-atk - at-spi2-core - ATK - ATLAS - atomate - AtomPAW - atools - atropos - ATSAS - attr - attrdict - attrdict3 - augur - AUGUSTUS - Austin - AUTO-07p - Autoconf - Autoconf-archive - AutoDock - AutoDock-GPU - AutoDock-Vina - AutoGeneS - AutoGrid - Automake - AutoMap - autopep8 - Autotools - Avogadro2 - avro-cpp - awscli
ABAQUS¶
Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.
homepage: http://www.simulia.com/products/abaqus_fea.html
version | versionsuffix | toolchain |
---|---|---|
6.12.1 |
-linux-x86_64 |
system |
6.13.5 |
-linux-x86_64 |
system |
6.14.1 |
-linux-x86_64 |
system |
2017 |
-hotfix-1721 |
system |
2018 |
-hotfix-1806 |
system |
2020 |
system |
|
2021 |
-hotfix-2132 |
system |
2022 |
system |
|
2022 |
-hotfix-2214 |
system |
2022 |
-hotfix-2223 |
system |
ABINIT¶
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
homepage: https://www.abinit.org/
version | versionsuffix | toolchain |
---|---|---|
7.0.3 |
-x86_64_linux_gnu4.5 |
system |
7.0.5 |
-x86_64_linux_gnu4.5 |
system |
7.2.1 |
-x86_64_linux_gnu4.5 |
system |
7.10.5 |
intel/2016.02-GCC-4.9 |
|
7.10.5 |
-libxc |
intel/2016.02-GCC-4.9 |
8.0.8 |
intel/2016a |
|
8.0.8b |
foss/2016b , intel/2016b |
|
8.2.2 |
foss/2016b , intel/2016b |
|
8.4.4 |
intel/2017b |
|
8.6.3 |
intel/2018a |
|
8.10.2 |
intel/2018b |
|
8.10.3 |
intel/2018b |
|
9.2.1 |
intel/2020a |
|
9.4.1 |
foss/2020b , intel/2020a , intel/2020b |
|
9.4.2 |
foss/2021a , intel/2021a |
|
9.6.2 |
foss/2022a , intel/2021a , intel/2021b , intel/2022a |
ABRA2¶
Assembly Based ReAligner
homepage: https://github.com/mozack/abra2
version | toolchain |
---|---|
2.22 |
iccifort/2019.5.281 |
2.23 |
GCC/10.2.0 , GCC/9.3.0 |
ABRicate¶
Mass screening of contigs for antimicrobial and virulence genes
homepage: https://github.com/tseemann/abricate
version | versionsuffix | toolchain |
---|---|---|
0.9.9 |
gompi/2019b |
|
0.9.9 |
-Perl-5.28.1 |
gompi/2019a |
1.0.0 |
gompi/2021a |
Abseil¶
Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.
homepage: https://abseil.io/
version | toolchain |
---|---|
20210324.2 |
GCCcore/11.2.0 |
20230125.2 |
GCCcore/12.2.0 |
20230125.3 |
GCCcore/12.3.0 |
abTEM¶
abTEM provides a Python API for running simulations of Transmission Electron Microscopy images.
homepage: https://github.com/jacobjma/abTEM
version | versionsuffix | toolchain |
---|---|---|
1.0.0b24 |
-ASE-3.22.0 |
fosscuda/2020b |
1.0.0b26 |
-ASE-3.22.0 |
foss/2020b , fosscuda/2020b |
ABySS¶
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss
version | toolchain |
---|---|
1.9.0 |
foss/2016a |
2.0.2 |
foss/2016b , foss/2018a , gompi/2019a , intel/2016b |
2.0.3 |
foss/2017b , intel/2017b |
2.1.5 |
foss/2019b |
2.2.5 |
foss/2020b |
ack¶
ack is a tool like grep, optimized for programmers
homepage: https://beyondgrep.com
version | toolchain |
---|---|
2.14 |
system |
3.4.0 |
GCCcore/10.2.0 |
3.5.0 |
GCCcore/10.3.0 |
ACT¶
ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format.
homepage: https://sanger-pathogens.github.io/Artemis/ACT/
version | versionsuffix | toolchain |
---|---|---|
18.0.2 |
-Java-11 |
system |
18.0.3 |
-Java-11 |
system |
ACTC¶
ACTC converts independent triangles into triangle strips or fans.
homepage: https://sourceforge.net/projects/actc
version | toolchain |
---|---|
1.1 |
GCCcore/10.2.0 , GCCcore/11.3.0 , GCCcore/6.4.0 , GCCcore/7.3.0 , GCCcore/8.3.0 , GCCcore/9.3.0 , intel/2016b |
ada¶
Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set.
homepage: https://cran.r-project.org/web/packages/ada/index.html
version | versionsuffix | toolchain |
---|---|---|
2.0-5 |
-R-3.4.0 |
intel/2017a |
AdapterRemoval¶
AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.
homepage: https://github.com/MikkelSchubert/adapterremoval
version | toolchain |
---|---|
2.2.0 |
foss/2016b |
2.2.2 |
foss/2018b |
2.3.1 |
foss/2018b |
2.3.2 |
GCC/10.2.0 , GCC/10.3.0 , GCC/11.2.0 |
2.3.3 |
GCC/11.3.0 |
ADDA¶
ADDA is an open-source parallel implementation of the discrete dipole approximation, capable to simulate light scattering by particles of arbitrary shape and composition in a wide range of particle sizes.
homepage: https://github.com/adda-team/adda/wiki
version | toolchain |
---|---|
1.3b4 |
foss/2019a |
ADF¶
ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT).
homepage: https://www.scm.com/ADF/
version | versionsuffix | toolchain |
---|---|---|
2009.01a.pc64_linux.intelmpi |
system |
|
2014.02 |
system |
|
2014.11.r48287 |
intel/2016a |
|
2016.101 |
system |
|
2019.303 |
-intelmpi |
system |
ADIOS¶
The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.
homepage: https://www.olcf.ornl.gov/center-projects/adios/
version | versionsuffix | toolchain |
---|---|---|
1.13.1 |
-Python-2.7.15 |
foss/2019a |
1.13.1 |
-Python-3.8.2 |
foss/2020a |
20210804 |
-Python-3.8.2 |
foss/2020a |
adjustText¶
A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.
homepage: https://github.com/Phlya/adjustText
version | versionsuffix | toolchain |
---|---|---|
0.7.3 |
foss/2021b |
|
0.7.3 |
-Python-3.6.6 |
foss/2018b |
0.7.3 |
-Python-3.7.2 |
intel/2019a |
ADMIXTURE¶
ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.
homepage: https://dalexander.github.io/admixture/
version | toolchain |
---|---|
1.3.0 |
system |
ADOL-C¶
The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C.
homepage: https://projects.coin-or.org/ADOL-C
version | toolchain |
---|---|
2.7.0 |
gompi/2019a |
2.7.2 |
gompi/2020a |
Advisor¶
Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
homepage: https://software.intel.com/intel-advisor-xe
version | toolchain |
---|---|
2016_update2 |
system |
2017_update1 |
system |
2018_update1 |
system |
2018_update3 |
system |
2019_update2 |
system |
2019_update3 |
system |
2019_update5 |
system |
2021.2.0 |
system |
2021.4.0 |
system |
2022.1.0 |
system |
AFNI¶
AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
homepage: http://afni.nimh.nih.gov/
version | versionsuffix | toolchain |
---|---|---|
18.1.09 |
-Python-3.6.4 |
intel/2018a |
18.3.00 |
-Python-3.6.6 |
foss/2018b |
19.0.01 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
20160329 |
-Python-2.7.11 |
intel/2016a |
AGAT¶
AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
homepage: https://agat.readthedocs.io/en/latest/
version | toolchain |
---|---|
0.9.2 |
GCC/11.2.0 |
AGeNT¶
The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software module that processes the read sequences from targeted high-throughput sequencing data generated by sequencing Agilent SureSelect and HaloPlex libraries. The Trimmer utility of the AGeNT module processes the read sequences to identify and remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with options to either mark or merge duplicate reads and output in BAM file format. The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
version | toolchain |
---|---|
3.0.6 |
system |
AGFusion¶
AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
homepage: https://github.com/murphycj/AGFusion
version | versionsuffix | toolchain |
---|---|---|
1.2 |
-Python-3.7.2 |
foss/2019a |
aiohttp¶
Asynchronous HTTP client/server framework for asyncio and Python.
homepage: https://github.com/aio-libs/aiohttp
version | versionsuffix | toolchain |
---|---|---|
3.5.4 |
-Python-3.6.6 |
foss/2018b |
3.8.1 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
|
3.8.3 |
GCCcore/11.3.0 |
ALADIN¶
ALADIN was entirely built on the notion of compatibility with its mother system, IFS/ARPEG. The latter, a joint development between the European Centre for Medium-Range Weather Forecasts (ECMWF) and Meteo-France, was only meant to consider global Numerical Weather Prediction applications; hence the idea, for ALADIN, to complement the IFS/ARPEGE project with a limited area model (LAM) version, while keeping the differences between the two softwares as small as possible.
homepage: http://www.cnrm.meteo.fr/aladin/
version | toolchain |
---|---|
36t1_op2bf1 |
intel/2016a |
Albacore¶
Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms.
version | versionsuffix | toolchain |
---|---|---|
2.0.2 |
-Python-3.6.1 |
intel/2017a |
Albumentations¶
Albumentations is a Python library for fast and flexible image augmentations
homepage: https://albumentations.ai
version | versionsuffix | toolchain |
---|---|---|
1.1.0 |
foss/2021b |
|
1.1.0 |
-CUDA-11.3.1 |
foss/2021a |
1.3.0 |
foss/2022a |
|
1.3.0 |
-CUDA-11.7.0 |
foss/2022a |
alevin-fry¶
alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
homepage: https://github.com/COMBINE-lab/alevin-fry
version | toolchain |
---|---|
0.4.3 |
GCCcore/11.2.0 |
0.6.0 |
GCCcore/10.3.0 |
ALFA¶
ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.
homepage: https://github.com/biocompibens/ALFA
version | versionsuffix | toolchain |
---|---|---|
1.1.1 |
-Python-3.7.2 |
foss/2019a |
Alfred¶
Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments.
homepage: https://www.gear-genomics.com/alfred/
version | toolchain |
---|---|
0.2.6 |
GCC/11.2.0 |
alleleCount¶
The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl code wraps the C implementation of allele counting code for BAM/CRAM processing.
homepage: http://cancerit.github.io/alleleCount/
version | toolchain |
---|---|
4.0.0 |
GCCcore/6.4.0 |
Allinea¶
The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.
homepage: http://www.allinea.com
version | toolchain |
---|---|
4.1-32834-Redhat-5.7-x86_64 |
system |
4.1-32834-Redhat-6.0-x86_64 |
system |
6.1.1-Ubuntu-14.04-x86_64 |
system |
ALLPATHS-LG¶
ALLPATHS-LG, the new short read genome assembler.
homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/
version | toolchain |
---|---|
52488 |
foss/2016a |
almosthere¶
Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program.
homepage: https://github.com/horta/almosthere
version | toolchain |
---|---|
1.0.1 |
GCCcore/7.3.0 |
1.0.10 |
GCCcore/9.3.0 |
2.0.2 |
GCCcore/10.2.0 |
Alpha¶
Alpha is a tool designed for detailed comparative study of bacteriophage genomes.
homepage: https://www.lirmm.fr/~swenson/alpha/alpha.htm
version | versionsuffix | toolchain |
---|---|---|
20200430 |
-Python-2.7.16 |
foss/2019b |
AlphaFold¶
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known. This package of AlphaFold contains patches for ColabFold.
homepage: https://github.com/sokrypton/alphafold
version | versionsuffix | toolchain |
---|---|---|
2.0.0 |
foss/2020b , fosscuda/2020b |
|
2.0.1 |
foss/2020b , fosscuda/2020b |
|
2.1.1 |
fosscuda/2020b |
|
2.1.2 |
foss/2021a |
|
2.1.2 |
-CUDA-11.3.1 |
foss/2021a |
2.1.2 |
-TensorFlow-2.5.0 |
foss/2020b , fosscuda/2020b |
2.2.2 |
foss/2021a |
|
2.2.2 |
-CUDA-11.3.1 |
foss/2021a |
2.3.0 |
-CUDA-11.4.1 |
foss/2021b |
2.3.1 |
foss/2022a |
|
2.3.1 |
-CUDA-11.7.0 |
foss/2022a |
2.3.4 |
-CUDA-11.7.0-ColabFold |
foss/2022a |
2.3.4 |
-ColabFold |
foss/2022a |
ALPS¶
The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code.
homepage: http://alps.comp-phys.org/
version | versionsuffix | toolchain |
---|---|---|
2.2.b4 |
-Python-2.7.11 |
intel/2016a |
2.3.0 |
-Python-2.7.12 |
foss/2016b |
2.3.0 |
-Python-3.5.2 |
foss/2016b |
alsa-lib¶
The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.
homepage: https://www.alsa-project.org
version | toolchain |
---|---|
1.2.4 |
GCCcore/9.3.0 |
1.2.8 |
GCCcore/10.2.0 , GCCcore/11.2.0 , GCCcore/11.3.0 |
AMAPVox¶
LiDAR data voxelisation software
homepage: https://amap-dev.cirad.fr/projects/amapvox
version | versionsuffix | toolchain |
---|---|---|
1.9.4 |
-Java-11 |
system |
Amara¶
Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML.
homepage: https://pypi.org/project/Amara
version | versionsuffix | toolchain |
---|---|---|
1.2.0.2 |
-Python-2.7.15 |
foss/2019a , intel/2019a |
amask¶
amask is a set of tools to to determine the affinity of MPI processes and OpenMP threads in a parallel environment.
homepage: https://github.com/TACC/amask
version | toolchain |
---|---|
20171106 |
foss/2018a |
20190404 |
foss/2018b |
Amber¶
Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
homepage: https://ambermd.org/amber.html
version | versionsuffix | toolchain |
---|---|---|
14 |
-AmberTools-15-patchlevel-13-13 |
intel/2016a |
16 |
-AmberTools-16-patchlevel-5-14 |
iomkl/2016.07 |
16 |
-AmberTools-16-patchlevel-5-14-CUDA |
iomkl/2016.09-GCC-4.9.3-2.25 |
16 |
-AmberTools-16-patchlevel-5-14-serial |
iomkl/2016.07 |
16 |
-AmberTools-17-patchlevel-10-15 |
foss/2018b , fosscuda/2018b , intel/2018b |
16 |
-AmberTools-17-patchlevel-10-15-Python-2.7.14 |
foss/2017b , fosscuda/2017b , intel/2017b , intelcuda/2017b |
16 |
-AmberTools-17-patchlevel-8-12 |
intel/2017b |
18 |
-AmberTools-18-patchlevel-10-8 |
foss/2018b , fosscuda/2018b , intel/2017b |
18 |
-AmberTools-19-patchlevel-12-17-Python-2.7.16 |
foss/2019b , fosscuda/2019b |
20.11 |
-AmberTools-20.15-Python-3.8.2 |
foss/2020a , fosscuda/2020a |
20.11 |
-AmberTools-21.3 |
foss/2020b , fosscuda/2020b |
22.0 |
-AmberTools-22.3 |
foss/2021b |
22.0 |
-AmberTools-22.3-CUDA-11.4.1 |
foss/2021b |
AmberMini¶
A stripped-down set of just antechamber, sqm, and tleap.
homepage: https://github.com/choderalab/ambermini
version | toolchain |
---|---|
16.16.0 |
intel/2017b , intel/2020a |
AmberTools¶
AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
homepage: https://ambermd.org/
version | versionsuffix | toolchain |
---|---|---|
17 |
intel/2017b , intel/2018a |
|
17 |
-Python-2.7.14 |
foss/2018a |
20 |
-Python-3.8.2 |
intel/2020a |
21 |
foss/2021a , intel/2021b |
|
21.12 |
foss/2021b |
|
22.3 |
foss/2021b |
AMD-LibM¶
AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines.
homepage: https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/
version | toolchain |
---|---|
3.2.2 |
GCC/7.3.0-2.30 |
3.6.0-4 |
GCC/9.3.0 |
AMD-RNG¶
AMD Random Number Generator Library is a pseudorandom number generator library.
homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/
version | toolchain |
---|---|
1.0 |
GCC/7.3.0-2.30 |
2.2-4 |
GCC/9.3.0 |
AMD-SecureRNG¶
The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation.
homepage: https://developer.amd.com/amd-cpu-libraries/rng-library/
version | toolchain |
---|---|
1.0 |
GCC/7.3.0-2.30 |
2.2-4 |
GCC/9.3.0 |
AMD-uProf¶
AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD operating systems. It allows developers to better understand the runtime performance of their application and to identify ways to improve its performance.
homepage: https://developer.amd.com/amd-uprof/
version | toolchain |
---|---|
3.4.502 |
system |
3.5.671 |
system |
AMOS¶
The AMOS consortium is committed to the development of open-source whole genome assembly software
homepage: http://amos.sourceforge.net
version | toolchain |
---|---|
3.1.0 |
foss/2018b , foss/2021b |
AMPHORA2¶
An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
homepage: https://github.com/wu-lab-uva/AMPHORA2
version | versionsuffix | toolchain |
---|---|---|
20190730 |
-Java-13-pthreads-avx2 |
gompi/2020b |
AMPL-MP¶
An open-source library for mathematical programming.
homepage: https://github.com/ampl/mp
version | toolchain |
---|---|
3.1.0 |
GCCcore/6.4.0 |
amplimap¶
amplimap is a command-line tool to automate the processing and analysis of data from targeted next-generation sequencing (NGS) experiments with PCR-based amplicons or capture-based enrichment systems.
homepage: https://amplimap.readthedocs.io/en/latest/
version | versionsuffix | toolchain |
---|---|---|
0.4.16 |
-Python-3.6.6 |
foss/2018b |
AMPtk¶
AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.
homepage: https://amptk.readthedocs.io
version | toolchain |
---|---|
1.5.4 |
foss/2021b |
AmrPlusPlus¶
AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database.
homepage: https://megares.meglab.org/amrplusplus/latest/html/v2
version | toolchain |
---|---|
2.0-20200114 |
GCC/8.3.0 |
AMS¶
The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics.
homepage: https://www.scm.com/amsterdam-modeling-suite/
version | versionsuffix | toolchain |
---|---|---|
2020.102 |
-intelmpi |
iimpi/2020b |
2022.102 |
-intelmpi |
iimpi/2021b |
Anaconda2¶
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
homepage: https://www.anaconda.com
version | toolchain |
---|---|
4.0.0 |
system |
4.2.0 |
system |
4.4.0 |
system |
5.0.1 |
system |
5.1.0 |
system |
5.3.0 |
system |
2018.12 |
system |
2019.03 |
system |
2019.07 |
system |
2019.10 |
system |
Anaconda3¶
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
homepage: https://www.anaconda.com
version | toolchain |
---|---|
4.0.0 |
system |
4.2.0 |
system |
4.4.0 |
system |
5.0.1 |
system |
5.1.0 |
system |
5.3.0 |
system |
2018.12 |
system |
2019.03 |
system |
2019.07 |
system |
2019.10 |
system |
2020.02 |
system |
2020.07 |
system |
2020.11 |
system |
2021.05 |
system |
2021.11 |
system |
2022.05 |
system |
2022.10 |
system |
aNCI¶
Non-covalent interaction (NCI) for MD trajectories
homepage: https://www.lct.jussieu.fr/pagesperso/contrera/nci-MD.html
version | toolchain |
---|---|
2.0 |
iccifort/2019.5.281 |
andi¶
This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
homepage: https://github.com/evolbioinf/andi/
version | toolchain |
---|---|
0.13 |
foss/2018b |
ANGEL¶
ANGEL: Robust Open Reading Frame prediction
homepage: https://github.com/PacificBiosciences/ANGEL
version | versionsuffix | toolchain |
---|---|---|
3.0 |
-Python-3.7.2 |
foss/2019a |
angsd¶
Program for analysing NGS data.
homepage: http://www.popgen.dk/angsd
version | toolchain |
---|---|
0.910 |
foss/2016a |
0.921 |
foss/2018a |
0.925 |
foss/2018b |
0.933 |
GCC/8.3.0 , iccifort/2019.5.281 |
0.935 |
GCC/10.2.0 |
0.940 |
GCC/11.2.0 |
ANIcalculator¶
This tool will calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.
homepage: https://ani.jgi.doe.gov/html/home.php
version | toolchain |
---|---|
1.0 |
GCCcore/10.3.0 , GCCcore/11.3.0 |
anndata¶
anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray
homepage: https://github.com/scverse/anndata
version | toolchain |
---|---|
0.8.0 |
foss/2022a |
Annif¶
Annif is a multi-algorithm automated subject indexing tool for libraries, archives and museums.
homepage: https://github.com/NatLibFi/Annif
version | versionsuffix | toolchain |
---|---|---|
0.40.0 |
-Python-3.7.2 |
foss/2019a , intel/2019a |
Annocript¶
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. Annocript also gives information about the longest ORF and the non-coding potential using external software. Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology and sequence features.
homepage: https://github.com/frankMusacchia/Annocript
version | toolchain |
---|---|
2.0 |
foss/2022a |
annovar¶
ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
homepage: http://annovar.openbioinformatics.org/en/latest/
version | versionsuffix | toolchain |
---|---|---|
2016Feb01 |
-Perl-5.22.1 |
foss/2016a |
20191024 |
-Perl-5.28.1 |
GCCcore/8.2.0 |
20200607 |
-Perl-5.34.0 |
GCCcore/11.2.0 |
ANSYS¶
ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
homepage: https://www.ansys.com
version | toolchain |
---|---|
15.0 |
system |
2022R2 |
system |
ANSYS_CFD¶
ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.
homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics
version | toolchain |
---|---|
16.2 |
system |
17.0 |
system |
ant¶
Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
homepage: http://ant.apache.org/
version | versionsuffix | toolchain |
---|---|---|
1.8.4 |
-Java-1.7.0_10 |
system |
1.8.4 |
-Java-1.7.0_21 |
system |
1.9.0 |
-Java-1.7.0_15 |
system |
1.9.0 |
-Java-1.7.0_21 |
system |
1.9.3 |
-Java-1.7.0_60 |
system |
1.9.3 |
-Java-1.7.0_79 |
system |
1.9.6 |
-Java-1.7.0_75 |
system |
1.9.6 |
-Java-1.7.0_79 |
system |
1.9.6 |
-Java-1.7.0_80 |
system |
1.9.6 |
-Java-1.8.0_66 |
system |
1.9.6 |
-Java-1.8.0_72 |
system |
1.9.6 |
-Java-1.8.0_77 |
system |
1.9.7 |
-Java-1.8.0_92 |
system |
1.10.0 |
-Java-1.8.0_112 |
system |
1.10.1 |
-Java-1.8 |
system |
1.10.1 |
-Java-1.8.0_121 |
system |
1.10.1 |
-Java-1.8.0_144 |
system |
1.10.1 |
-Java-1.8.0_152 |
system |
1.10.1 |
-Java-1.8.0_162 |
system |
1.10.5 |
-Java-1.8 |
system |
1.10.6 |
-Java-1.8 |
system |
1.10.7 |
-Java-11 |
system |
1.10.8 |
-Java-11 |
system |
1.10.9 |
-Java-11 |
system |
1.10.11 |
-Java-11 |
system |
1.10.11 |
-Java-13 |
system |
1.10.12 |
-Java-11 |
system |
1.10.12 |
-Java-17 |
system |
antiSMASH¶
antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
homepage: https://github.com/antismash/antismash
version | versionsuffix | toolchain |
---|---|---|
5.1.2 |
-Python-3.7.4 |
foss/2019b |
5.2.0 |
foss/2020b |
|
6.0.1 |
foss/2020b |
ANTLR¶
ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.
homepage: http://www.antlr2.org/
version | versionsuffix | toolchain |
---|---|---|
2.7.7 |
GCCcore/7.3.0 , GCCcore/8.2.0 , foss/2017b , foss/2018b , foss/2019a , intel/2017b |
|
2.7.7 |
-Java-11 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
2.7.7 |
-Python-2.7.11 |
foss/2016a |
2.7.7 |
-Python-2.7.13 |
intel/2017a |
2.7.7 |
-Python-2.7.14 |
foss/2018a , intel/2017b |
2.7.7 |
-Python-3.6.4 |
intel/2018a |
ANTs¶
ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
homepage: https://stnava.github.io/ANTs/
version | versionsuffix | toolchain |
---|---|---|
2.2.0 |
-Python-2.7.12 |
foss/2016b |
2.3.0 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
2.3.1 |
-Python-3.6.6 |
foss/2018b |
2.3.2 |
-Python-3.7.4 |
foss/2019b |
2.3.5 |
foss/2021a |
anvio¶
An analysis and visualization platform for 'omics data.
homepage: https://merenlab.org/software/anvio/
version | versionsuffix | toolchain |
---|---|---|
6.1 |
-Python-3.7.4 |
intel/2019b |
any2fasta¶
Convert various sequence formats to FASTA
homepage: https://github.com/tseemann/any2fasta
version | versionsuffix | toolchain |
---|---|---|
0.4.2 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
|
0.4.2 |
-Perl-5.28.1 |
GCCcore/8.2.0 |
AOCC¶
AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0
homepage: https://developer.amd.com/amd-aocc/
version | toolchain |
---|---|
2.3.0 |
GCCcore/10.2.0 , GCCcore/9.3.0 |
3.0.0 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
3.1.0 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 |
3.2.0 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
4.0.0 |
GCCcore/11.3.0 , GCCcore/12.2.0 |
AOMP¶
AMD fork of LLVM, setup for OpenMP offloading to Accelerators
homepage: https://github.com/ROCm-Developer-Tools/aomp
version | toolchain |
---|---|
13.0-2 |
GCCcore/10.2.0 , gcccuda/2020a |
APBS¶
APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.
homepage: http://www.poissonboltzmann.org/apbs
version | versionsuffix | toolchain |
---|---|---|
1.4 |
-linux-static-x86_64 |
system |
apex¶
A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch
homepage: https://github.com/nvidia/apex
version | versionsuffix | toolchain |
---|---|---|
20200325 |
-Python-3.7.4 |
fosscuda/2019b |
20210420 |
fosscuda/2020b |
APR¶
Apache Portable Runtime (APR) libraries.
homepage: https://apr.apache.org/
version | toolchain |
---|---|
1.6.3 |
GCCcore/6.4.0 , GCCcore/7.3.0 , iomkl/2018a |
1.7.0 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/8.2.0 , GCCcore/9.3.0 |
APR-util¶
Apache Portable Runtime (APR) util libraries.
homepage: http://apr.apache.org/
version | toolchain |
---|---|
1.6.1 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/6.4.0 , GCCcore/7.3.0 , GCCcore/8.2.0 , GCCcore/9.3.0 , iomkl/2018a |
AptaSUITE¶
A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments
homepage: https://drivenbyentropy.github.io/
version | versionsuffix | toolchain |
---|---|---|
0.9.4 |
-Java-11 |
system |
ARAGORN¶
a program to detect tRNA genes and tmRNA genes in nucleotide sequences
homepage: http://www.ansikte.se/ARAGORN/
version | toolchain |
---|---|
1.2.38 |
foss/2016b , iccifort/2019.5.281 |
1.2.41 |
foss/2021b |
Arb¶
Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested.
homepage: https://arblib.org/
version | toolchain |
---|---|
2.16.0 |
GCC/7.3.0-2.30 , GCC/8.2.0-2.31.1 , iccifort/2018.3.222-GCC-7.3.0-2.30 |
2.17.0 |
GCC/8.3.0 |
2.19.0 |
GCC/10.3.0 |
2.22.1 |
foss/2021b |
2.23.0 |
gfbf/2022a |
Arcade-Learning-Environment¶
The Arcade Learning Environment (ALE) is a simple framework that allows researchers and hobbyists to develop AI agents for Atari 2600 games. It is built on top of the Atari 2600 emulator Stella and separates the details of emulation from agent design. This video depicts over 50 games currently supported in the ALE.
homepage: https://github.com/mgbellemare/Arcade-Learning-Environment
version | toolchain |
---|---|
0.7.3 |
foss/2021b |
arcasHLA¶
arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
homepage: https://github.com/RabadanLab/arcasHLA
version | versionsuffix | toolchain |
---|---|---|
0.2.0 |
-Python-3.7.4 |
foss/2019b |
ARCH¶
Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financial econometrics, written in Python (with Cython and/or Numba used to improve performance).
homepage: https://pypi.org/project/arch
version | versionsuffix | toolchain |
---|---|---|
4.5.0 |
-Python-3.6.4 |
intel/2018a |
Archive-Zip¶
Provide an interface to ZIP archive files.
homepage: https://metacpan.org/pod/Archive::Zip
version | toolchain |
---|---|
1.68 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 |
ArchR¶
ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data.
homepage: https://www.archrproject.com
version | versionsuffix | toolchain |
---|---|---|
1.0.1 |
-R-4.1.2 |
foss/2021b |
archspec¶
A library for detecting, labeling, and reasoning about microarchitectures
homepage: https://github.com/archspec/archspec
version | versionsuffix | toolchain |
---|---|---|
0.1.0 |
-Python-3.7.4 |
GCCcore/8.3.0 |
0.1.0 |
-Python-3.8.2 |
GCCcore/9.3.0 |
0.1.2 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
|
0.1.3 |
GCCcore/11.2.0 |
|
0.1.4 |
GCCcore/11.3.0 |
|
0.2.0 |
GCCcore/12.2.0 |
ARGoS¶
A parallel, multi-engine simulator for heterogeneous swarm robotics
homepage: http://www.argos-sim.info
version | versionsuffix | toolchain |
---|---|---|
3.0.0-beta53 |
-Lua-5.2.4 |
foss/2018b |
3.0.0-beta59 |
GCC/11.2.0 |
argtable¶
Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
homepage: http://argtable.sourceforge.net/
version | toolchain |
---|---|
2.13 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/8.2.0 , GCCcore/8.3.0 , foss/2016b , foss/2018b , intel/2018a , intel/2018b |
aria2¶
aria2 is a lightweight multi-protocol & multi-source command-line download utility.
homepage: https://aria2.github.io
version | toolchain |
---|---|
1.35.0 |
GCCcore/10.3.0 |
1.36.0 |
GCCcore/11.3.0 |
Arlequin¶
Arlequin: An Integrated Software for Population Genetics Data Analysis
homepage: http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html
version | toolchain |
---|---|
3.5.2.2 |
foss/2019b |
Armadillo¶
Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
homepage: https://arma.sourceforge.net/
version | versionsuffix | toolchain |
---|---|---|
7.600.2 |
-Python-2.7.12 |
foss/2016b |
7.800.0 |
-Python-2.7.12 |
intel/2016b |
7.950.1 |
-Python-2.7.12 |
intel/2016b |
8.300.1 |
foss/2017b , intel/2017b |
|
8.400.0 |
foss/2018a |
|
9.600.5 |
foss/2018b |
|
9.700.2 |
foss/2019a |
|
9.880.1 |
foss/2020a |
|
9.900.1 |
foss/2019b , foss/2020a |
|
10.5.3 |
foss/2020b |
|
10.7.5 |
foss/2021a |
|
11.4.3 |
foss/2022a , foss/2022b |
arosics¶
AROSICS is a python package to perform automatic subpixel co-registration of two satellite image datasets based on an image matching approach working in the frequency domain, combined with a multistage workflow for effective detection of false-positives.
homepage: https://github.com/GFZ/arosics
version | toolchain |
---|---|
1.7.6 |
foss/2021a |
ARPACK++¶
Arpackpp is a C++ interface to the ARPACK Fortran package, which implements the implicit restarted Arnoldi method for iteratively solving large-scale sparse eigenvalue problems.
homepage: https://github.com/m-reuter/arpackpp
version | toolchain |
---|---|
2018.03.26 |
foss/2017b |
arpack-ng¶
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
homepage: https://github.com/opencollab/arpack-ng
version | toolchain |
---|---|
3.3.0 |
foss/2016a , intel/2016a |
3.4.0 |
foss/2016b , foss/2017a , intel/2016b , intel/2017a |
3.5.0 |
foss/2017b , foss/2018a , foss/2018b , intel/2017a , intel/2017b |
3.6.2 |
intel/2018a |
3.7.0 |
foss/2019a , foss/2019b , foss/2020a , intel/2019b , intel/2020a |
3.8.0 |
foss/2020b , foss/2021a , foss/2021b , foss/2022a , foss/2022b |
ArrayFire¶
ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.
homepage: https://arrayfire.com/
version | versionsuffix | toolchain |
---|---|---|
3.6.4 |
foss/2018b |
|
3.6.4 |
-CUDA-9.2.88 |
foss/2018b |
Arriba¶
Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.
homepage: https://github.com/suhrig/arriba
version | toolchain |
---|---|
1.1.0 |
foss/2018b |
2.1.0 |
GCC/10.2.0 , GCC/10.3.0 |
2.2.1 |
GCC/11.2.0 |
2.3.0 |
GCC/11.2.0 |
Arrow¶
Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.
homepage: https://arrow.apache.org
version | versionsuffix | toolchain |
---|---|---|
0.7.1 |
-Python-3.6.3 |
intel/2017b |
0.12.0 |
-Python-2.7.15 |
foss/2018b , intel/2018b |
0.12.0 |
-Python-3.6.6 |
intel/2018b |
0.16.0 |
-Python-3.7.4 |
foss/2019b , intel/2019b |
0.17.1 |
foss/2020b , fosscuda/2020b , intel/2020b |
|
0.17.1 |
-Python-3.8.2 |
foss/2020a , intel/2020a |
6.0.0 |
foss/2021a , foss/2021b |
|
6.0.1 |
foss/2021a |
|
8.0.0 |
foss/2022.05 , foss/2022a |
|
11.0.0 |
gfbf/2022b |
arrow-R¶
R interface to the Apache Arrow C++ library
homepage: https://cran.r-project.org/web/packages/arrow
version | versionsuffix | toolchain |
---|---|---|
0.17.1 |
-R-4.0.0 |
foss/2020a |
6.0.0.2 |
-R-4.1.0 |
foss/2021a |
6.0.0.2 |
-R-4.1.2 |
foss/2021b |
6.0.0.2 |
-R-4.2.0 |
foss/2021b |
8.0.0 |
-R-4.2.1 |
foss/2022a |
11.0.0.3 |
-R-4.2.2 |
foss/2022b |
ART¶
ART is a set of simulation tools to generate synthetic next-generation sequencing reads
homepage: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
version | toolchain |
---|---|
2016.06.05 |
GCCcore/6.4.0 , intel/2016b |
artic-ncov2019¶
Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus.
homepage: https://github.com/artic-network/artic-ncov2019
version | versionsuffix | toolchain |
---|---|---|
2020.04.13 |
-Python-3.6.6 |
foss/2018b |
2021.06.24 |
foss/2020b |
ARTS¶
ARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly for the different sensors.
homepage: http://www.radiativetransfer.org/
version | toolchain |
---|---|
2.2.64 |
gompi/2019a |
ArviZ¶
Exploratory analysis of Bayesian models with Python
homepage: https://github.com/arviz-devs/arviz
version | versionsuffix | toolchain |
---|---|---|
0.7.0 |
-Python-3.7.4 |
foss/2019b , intel/2019b |
0.11.1 |
intel/2020b |
|
0.11.4 |
foss/2021b , intel/2021b |
|
0.12.1 |
foss/2022a , intel/2022a |
ARWEN¶
ARWEN, tRNA detection in metazoan mitochondrial sequences
homepage: http://mbio-serv2.mbioekol.lu.se/ARWEN
version | toolchain |
---|---|
1.2.3 |
GCCcore/7.3.0 |
ASAP¶
ASAP focuses on fast and fluid image viewing with an easy-to-use interface for making annotations. It consists of two main components: an IO library for reading and writing multi-resolution images and a viewer component for visualizing such images.
homepage: https://computationalpathologygroup.github.io/ASAP/
version | versionsuffix | toolchain |
---|---|---|
2.0 |
-CUDA-11.3.1 |
foss/2021a |
2.1 |
foss/2022a |
ASAP3¶
ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE).
homepage: https://wiki.fysik.dtu.dk/asap/
version | versionsuffix | toolchain |
---|---|---|
3.10.7 |
-Python-3.5.2 |
foss/2016b |
3.10.7 |
-Python-3.6.2 |
foss/2017b |
3.10.8 |
-Python-3.5.2 |
foss/2016b |
3.10.8 |
-Python-3.6.2 |
foss/2017b |
3.10.8 |
-Python-3.6.3 |
foss/2017b |
3.10.10 |
-Python-3.6.6 |
foss/2018b , intel/2018b , iomkl/2018b |
3.11.10 |
-Python-3.7.2 |
foss/2019a , intel/2019a |
3.12.2 |
-ASE-3.21.1 |
foss/2020b , intel/2020b |
3.12.7 |
-ASE-3.21.1 |
foss/2020b , intel/2020b |
ASE¶
ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language.
homepage: https://wiki.fysik.dtu.dk/ase/
version | versionsuffix | toolchain |
---|---|---|
3.9.1.4567 |
-Python-2.7.11 |
intel/2016a |
3.10.0 |
-Python-2.7.11 |
intel/2016.02-GCC-4.9 |
3.11.0 |
-Python-2.7.12 |
intel/2016b |
3.13.0 |
-Python-2.7.12 |
foss/2016b |
3.13.0 |
-Python-2.7.13 |
intel/2017a |
3.15.0 |
-Python-2.7.12 |
foss/2016b |
3.15.0 |
-Python-2.7.14 |
intel/2017b |
3.15.0 |
-Python-3.5.2 |
foss/2016b |
3.15.0 |
-Python-3.6.2 |
foss/2017b |
3.15.0 |
-Python-3.6.3 |
foss/2017b |
3.16.2 |
-Python-3.6.4 |
iomkl/2018.02 , iomkl/2018a |
3.16.2 |
-Python-3.6.6 |
foss/2018b , intel/2018b , iomkl/2018b |
3.17.0 |
-Python-3.6.6 |
foss/2018b , intel/2018b , iomkl/2018b |
3.17.0 |
-Python-3.7.2 |
foss/2019a , intel/2019a |
3.18.0 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
3.18.0 |
-Python-3.7.2 |
foss/2019a , intel/2019a |
3.19.0 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
3.19.0 |
-Python-3.7.4 |
foss/2019b , fosscuda/2019b , intel/2019b |
3.19.0 |
-Python-3.8.2 |
foss/2020a , intel/2020a |
3.20.1 |
foss/2020b , fosscuda/2020b , intel/2020b |
|
3.20.1 |
-Python-3.7.4 |
foss/2019b , intel/2019b |
3.20.1 |
-Python-3.8.2 |
intel/2020a |
3.21.1 |
foss/2020b , fosscuda/2020b , intel/2020b |
|
3.21.1 |
-Python-3.8.2 |
foss/2020a |
3.22.0 |
foss/2020b , foss/2021a , fosscuda/2020b , intel/2020b , intel/2021a |
|
3.22.1 |
foss/2021b , foss/2022a , gfbf/2022b , gomkl/2021a , intel/2021b , intel/2022a |
ASHS¶
Automatic Segmentation of Hippocampal Subfields (ASHS)
homepage: https://sites.google.com/site/hipposubfields/home
version | toolchain |
---|---|
rev103_20140612 |
system |
Aspera-CLI¶
IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.
homepage: https://asperasoft.com
version | versionsuffix | toolchain |
---|---|---|
3.7.2 |
.354.010c3b8 |
system |
3.9.0 |
.1326.6985b21 |
system |
3.9.6 |
.1467.159c5b1 |
system |
Aspera-Connect¶
Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.
homepage: http://downloads.asperasoft.com/connect2/
version | toolchain |
---|---|
3.6.1 |
system |
3.9.6 |
system |
assimp¶
Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data.
homepage: https://github.com/assimp/assimp
version | toolchain |
---|---|
5.0.1 |
GCCcore/8.3.0 |
Assimulo¶
Assimulo is a simulation package for solving ordinary differential equations.
homepage: https://jmodelica.org/assimulo/
version | versionsuffix | toolchain |
---|---|---|
2.9 |
-Python-2.7.15 |
intel/2018b |
ASTRID¶
ASTRID-2 is a method for estimating species trees from gene trees.
homepage: https://github.com/pranjalv123/ASTRID
version | toolchain |
---|---|
2.2.1 |
gompi/2019a |
astro-tulips¶
tulips creates diagrams of the structure and evolution of stars. It creates plots and movies based on output from the MESA stellar evolution code
homepage: https://astro-tulips.readthedocs.io/en/latest/installation.html
version | toolchain |
---|---|
1.0.1 |
foss/2022a |
astropy¶
The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages. The Astropy community is committed to supporting diversity and inclusion.
homepage: https://www.astropy.org/
version | versionsuffix | toolchain |
---|---|---|
2.0.12 |
-Python-2.7.15 |
foss/2018b , intel/2018b |
2.0.14 |
foss/2019a |
|
4.0.1 |
-Python-3.7.4 |
foss/2019b |
4.0.1 |
-Python-3.8.2 |
foss/2020a , intel/2020a |
4.2.1 |
foss/2020b , intel/2020b , intelcuda/2020b |
|
4.3.1 |
foss/2021a , foss/2021b , intel/2021a |
|
5.0.4 |
foss/2021a |
|
5.1.1 |
foss/2022a |
|
5.2.2 |
gfbf/2022b |
at-spi2-atk¶
AT-SPI 2 toolkit bridge
homepage: https://wiki.gnome.org/Accessibility
version | toolchain |
---|---|
2.26.3 |
fosscuda/2018b |
2.32.0 |
GCCcore/8.2.0 |
2.34.1 |
GCCcore/8.3.0 |
2.34.2 |
GCCcore/9.3.0 |
2.38.0 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/12.2.0 |
at-spi2-core¶
Assistive Technology Service Provider Interface.
homepage: https://wiki.gnome.org/Accessibility
version | toolchain |
---|---|
2.26.3 |
fosscuda/2018b |
2.32.0 |
GCCcore/8.2.0 |
2.34.0 |
GCCcore/8.3.0 |
2.36.0 |
GCCcore/9.3.0 |
2.38.0 |
GCCcore/10.2.0 |
2.40.2 |
GCCcore/10.3.0 |
2.40.3 |
GCCcore/11.2.0 |
2.44.1 |
GCCcore/11.3.0 |
2.46.0 |
GCCcore/12.2.0 |
ATK¶
ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
homepage: https://developer.gnome.org/atk/
version | toolchain |
---|---|
2.18.0 |
intel/2016a |
2.20.0 |
foss/2016a , intel/2016a |
2.22.0 |
foss/2016b , intel/2016b |
2.26.0 |
intel/2017a |
2.26.1 |
foss/2018b , intel/2017b |
2.27.1 |
foss/2017b , intel/2017b |
2.28.1 |
foss/2018a , foss/2018b , fosscuda/2018b , intel/2018a |
2.32.0 |
GCCcore/8.2.0 |
2.34.1 |
GCCcore/8.3.0 |
2.36.0 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/9.3.0 |
2.38.0 |
GCCcore/11.3.0 , GCCcore/12.2.0 |
ATLAS¶
ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library.
homepage: http://math-atlas.sourceforge.net
version | versionsuffix | toolchain |
---|---|---|
3.10.2 |
-LAPACK-3.6.1 |
GCC/5.4.0-2.26 |
atomate¶
atomate has implementations of FireWorks workflows for Materials Science.
homepage: https://pythonhosted.org/atomate/
version | versionsuffix | toolchain |
---|---|---|
0.4.4 |
-Python-2.7.13 |
intel/2017a |
AtomPAW¶
AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library.
homepage: http://users.wfu.edu/natalie/papers/pwpaw/man.html
version | toolchain |
---|---|
4.1.0.5 |
intel/2018b |
4.1.0.6 |
intel/2018b |
atools¶
Tools to make using job arrays a lot more convenient.
homepage: https://github.com/gjbex/atools
version | versionsuffix | toolchain |
---|---|---|
1.4.2 |
-Python-2.7.12 |
intel/2016b |
1.4.6 |
-Python-2.7.16 |
GCCcore/8.3.0 |
1.4.8 |
-Python-2.7.18 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
1.5.1 |
GCCcore/11.2.0 |
atropos¶
Atropos is tool for specific, sensitive, and speedy trimming of NGS reads.
homepage: https://atropos.readthedocs.io
version | versionsuffix | toolchain |
---|---|---|
1.1.21 |
-Python-3.6.6 |
intel/2018b |
ATSAS¶
ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.
homepage: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html
version | versionsuffix | toolchain |
---|---|---|
2.5.1-1 |
.el6.x86_64 |
system |
2.5.1-1 |
.sl5.x86_64 |
system |
2.7.1-1 |
.el7.x86_64 |
system |
attr¶
Commands for Manipulating Filesystem Extended Attributes
homepage: https://savannah.nongnu.org/projects/attr
version | toolchain |
---|---|
2.4.47 |
GCCcore/8.2.0 |
2.4.48 |
GCCcore/9.3.0 |
2.5.1 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
attrdict¶
AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.
homepage: https://github.com/bcj/AttrDict
version | versionsuffix | toolchain |
---|---|---|
2.0.1 |
-Python-3.7.4 |
GCCcore/8.3.0 |
attrdict3¶
AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.
homepage: https://github.com/pirofti/AttrDict3
version | toolchain |
---|---|
2.0.2 |
GCCcore/11.2.0 |
augur¶
Pipeline components for real-time phylodynamic analysis
homepage: https://github.com/nextstrain/augur
version | versionsuffix | toolchain |
---|---|---|
7.0.2 |
-Python-3.7.4 |
intel/2019b |
AUGUSTUS¶
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
homepage: https://bioinf.uni-greifswald.de/augustus/
version | versionsuffix | toolchain |
---|---|---|
3.2.3 |
-Python-2.7.13 |
intel/2017a |
3.3 |
foss/2018a |
|
3.3.2 |
intel/2019a |
|
3.3.2 |
-Python-2.7.13 |
intel/2017a |
3.3.2 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
3.3.2 |
-Python-2.7.15 |
intel/2018b |
3.3.3 |
foss/2019b , intel/2019b |
|
3.4.0 |
foss/2020a , foss/2020b , foss/2021a , foss/2021b |
|
3.5.0 |
foss/2022a |
Austin¶
Austin is a Python frame stack sampler for CPython written in pure C.
homepage: https://github.com/P403n1x87/austin
version | toolchain |
---|---|
3.2.0 |
GCCcore/11.2.0 , system |
AUTO-07p¶
AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.
homepage: https://github.com/auto-07p
version | toolchain |
---|---|
0.9.3 |
foss/2021a |
Autoconf¶
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
homepage: https://www.gnu.org/software/autoconf/
version | toolchain |
---|---|
2.68 |
foss/2016b |
2.69 |
GCC/4.8.2 , GCC/4.8.4 , GCC/4.9.2 , GCC/4.9.3 , GCC/4.9.3-2.25 , GCC/5.2.0 , GCC/5.4.0-2.26 , GCCcore/10.2.0 , GCCcore/4.9.2 , GCCcore/4.9.3 , GCCcore/5.3.0 , GCCcore/5.4.0 , GCCcore/6.1.0 , GCCcore/6.2.0 , GCCcore/6.3.0 , GCCcore/6.4.0 , GCCcore/7.2.0 , GCCcore/7.3.0 , GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.2.0 , GCCcore/9.3.0 , GNU/4.9.2-2.25 , GNU/4.9.3-2.25 , GNU/5.1.0-2.25 , foss/2016.04 , foss/2016a , foss/2016b , gimkl/2.11.5 , intel/2016.02-GCC-4.9 , intel/2016a , intel/2016b , iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 , system |
2.71 |
FCC/4.5.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/12.2.0 , system |
Autoconf-archive¶
The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software.
homepage: https://www.gnu.org/software/autoconf-archive
version | toolchain |
---|---|
2019.01.06 |
GCC/8.2.0-2.31.1 |
2021.02.19 |
GCCcore/10.2.0 |
AutoDock¶
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
homepage: http://autodock.scripps.edu/
version | toolchain |
---|---|
4.2.5.1 |
GCC/5.2.0 |
4.2.6 |
GCC/10.3.0 |
AutoDock-GPU¶
OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
homepage: https://github.com/ccsb-scripps/AutoDock-GPU
version | versionsuffix | toolchain |
---|---|---|
1.5.3 |
-CUDA-11.3.1 |
GCC/10.3.0 |
AutoDock-Vina¶
AutoDock Vina is an open-source program for doing molecular docking.
homepage: https://vina.scripps.edu/
version | versionsuffix | toolchain |
---|---|---|
1.1.2 |
-linux_x86 |
system |
1.2.3 |
foss/2021a , foss/2021b |
AutoGeneS¶
AutoGeneS automatically extracts informative genes and reveals the cellular heterogeneity of bulk RNA samples.
homepage: https://github.com/theislab/AutoGeneS
version | toolchain |
---|---|
1.0.4 |
foss/2020b |
AutoGrid¶
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
homepage: http://autodock.scripps.edu/
version | toolchain |
---|---|
4.2.5.1 |
GCC/5.2.0 |
Automake¶
Automake: GNU Standards-compliant Makefile generator
homepage: https://www.gnu.org/software/automake/automake.html
version | toolchain |
---|---|
1.11.3 |
foss/2016b |
1.14 |
GCC/4.8.2 , intel/2016a |
1.14.1 |
GCC/4.8.2 |
1.15 |
GCC/4.8.4 , GCC/4.9.2 , GCC/4.9.3 , GCC/4.9.3-2.25 , GCC/5.2.0 , GCC/5.4.0-2.26 , GCCcore/4.9.2 , GCCcore/4.9.3 , GCCcore/5.3.0 , GCCcore/5.4.0 , GCCcore/6.1.0 , GCCcore/6.2.0 , GCCcore/6.3.0 , GNU/4.9.2-2.25 , GNU/4.9.3-2.25 , GNU/5.1.0-2.25 , foss/2016.04 , foss/2016a , foss/2016b , gimkl/2.11.5 , intel/2016.02-GCC-4.9 , intel/2016a , intel/2016b , iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 , system |
1.15.1 |
GCCcore/6.4.0 , GCCcore/7.2.0 , GCCcore/7.3.0 , GCCcore/8.3.0 |
1.16.1 |
GCCcore/6.4.0 , GCCcore/7.3.0 , GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.2.0 , GCCcore/9.3.0 |
1.16.2 |
GCCcore/10.2.0 |
1.16.3 |
FCC/4.5.0 , GCCcore/10.3.0 |
1.16.4 |
GCCcore/11.2.0 |
1.16.5 |
GCCcore/11.3.0 , GCCcore/12.2.0 , system |
AutoMap¶
Tool to find regions of homozygosity (ROHs) from sequencing data.
homepage: https://github.com/mquinodo/AutoMap
version | versionsuffix | toolchain |
---|---|---|
1.0 |
-20200324 |
foss/2019b |
autopep8¶
A tool that automatically formats Python code to conform to the PEP 8 style guide.
homepage: https://github.com/hhatto/autopep8
version | versionsuffix | toolchain |
---|---|---|
1.4.4 |
-Python-3.6.4 |
intel/2018a |
Autotools¶
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
homepage: https://autotools.io
version | toolchain |
---|---|
20150119 |
GCC/4.9.2 |
20150215 |
GCC/4.8.4 , GCC/4.9.2 , GCC/4.9.3 , GCC/4.9.3-2.25 , GCC/5.2.0 , GCC/5.4.0-2.26 , GCCcore/4.9.2 , GCCcore/4.9.3 , GCCcore/5.3.0 , GCCcore/5.4.0 , GCCcore/6.1.0 , GCCcore/6.2.0 , GCCcore/6.3.0 , GNU/4.9.2-2.25 , GNU/4.9.3-2.25 , GNU/5.1.0-2.25 , foss/2016.04 , foss/2016a , foss/2016b , gimkl/2.11.5 , gimkl/2017a , intel/2016.02-GCC-4.9 , intel/2016a , intel/2016b , iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 , system |
20170619 |
GCCcore/6.4.0 , GCCcore/7.2.0 |
20180311 |
GCCcore/7.3.0 , GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.2.0 , GCCcore/9.3.0 |
20200321 |
GCCcore/10.2.0 |
20210128 |
FCC/4.5.0 , GCCcore/10.3.0 |
20210726 |
GCCcore/11.2.0 |
20220317 |
GCCcore/11.3.0 , GCCcore/12.2.0 , system |
Avogadro2¶
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
homepage: https://two.avogadro.cc/index.html
version | versionsuffix | toolchain |
---|---|---|
1.97.0 |
-linux-x86_64 |
system |
avro-cpp¶
C++ implementation of Avro data serialization system.
homepage: https://avro.apache.org
version | toolchain |
---|---|
1.11.1 |
GCC/11.2.0 |
awscli¶
Universal Command Line Environment for AWS
homepage: https://pypi.python.org/pypi/awscli
version | versionsuffix | toolchain |
---|---|---|
1.11.1 |
-Python-2.7.12 |
intel/2016b |
1.11.56 |
-Python-2.7.12 |
foss/2016b |
1.16.290 |
-Python-3.6.6 |
foss/2018b |
1.17.7 |
-Python-3.7.4 |
GCCcore/8.3.0 |
1.18.89 |
-Python-3.8.2 |
GCCcore/9.3.0 |
2.0.55 |
-Python-3.8.2 |
GCCcore/9.3.0 |
2.11.21 |
GCCcore/11.3.0 |
B¶
BA3-SNPS-autotune - BabelStream - babl - Bader - BAGEL - BAli-Phy - bam-readcount - Bambi - bamFilters - BAMM - BAMSurgeon - bamtofastq - BamTools - BamUtil - Bandage - barrnap - basemap - Bash - bashplotlib - bat - batchgenerators - BatMeth2 - BayesAss - BayesAss3-SNPs - BayeScan - BayeScEnv - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - bcbio-gff - BCEL - BCFtools - bcgTree - bcl-convert - bcl2fastq2 - bcolz - BDBag - Beagle - beagle-lib - Beast - BeautifulSoup - BEDOPS - BEDTools - BEEF - behave - BerkeleyGW - BFAST - BFC - bgen - bgen-reader - bibtexparser - BiG-SCAPE - BigDFT - BinSanity - binutils - Bio-DB-HTS - Bio-EUtilities - Bio-SamTools - Bio-SearchIO-hmmer - bioawk - biobambam2 - biogeme - biom-format - biomart-perl - BioPerl - BioPP - Biopython - BioServices - BirdNET - biscuit - Bismark - Bison - bitarray - BLACS - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - BLIS - Blitz++ - BlobTools - Block - Blosc - Blosc2 - BLT - bmtagger - bnpy - BOINC - bokeh - BoltzTraP - BoltzTraP2 - Bonito - Bonmin - Bonnie++ - Boost - Boost.MPI - Boost.Python - boost_histogram - boto3 - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp - bpytop - Bracken - Braindecode - BRAKER - BreakDancer - breseq - Brotli - Brotli-python - Brunsli - bsddb3 - BSMAPz - Bsoft - BSseeker2 - BuDDy - BUFRLIB - build - buildenv - buildingspy - Bullet - BUSCO - BUStools - BWA - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - byobu - bzip2
BA3-SNPS-autotune¶
This program will automatically tune mixing parameters for BA3-SNPs by implementing a binary search algorithm and conducting short exploratory runs of BA3-SNPS.
homepage: https://github.com/stevemussmann/BA3-SNPS-autotune
version | toolchain |
---|---|
2.1.2 |
GCC/11.3.0 |
BabelStream¶
STREAM, for lots of devices written in many programming models
homepage: https://uob-hpc.github.io/BabelStream
version | versionsuffix | toolchain |
---|---|---|
3.4 |
-omp |
GCC/11.2.0 |
babl¶
babl is pixel encoding and color space conversion engine in C
homepage: https://www.gegl.org/babl
version | toolchain |
---|---|
0.1.86 |
GCCcore/10.3.0 |
Bader¶
A fast algorithm for doing Bader's analysis on a charge density grid.
homepage: http://theory.cm.utexas.edu/henkelman/code/bader/
version | toolchain |
---|---|
1.02 |
intel/2018a |
1.03 |
intel/2018b |
1.04 |
GCC/11.2.0 , iccifort/2020.4.304 |
BAGEL¶
BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program.
homepage: http://www.nubakery.org
version | toolchain |
---|---|
1.1.1 |
intel/2016b |
BAli-Phy¶
BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences.
homepage: http://www.bali-phy.org/
version | toolchain |
---|---|
3.6.0 |
system |
bam-readcount¶
Count DNA sequence reads in BAM files
homepage: https://github.com/genome/bam-readcount
version | toolchain |
---|---|
0.8.0 |
GCC/11.2.0 , GCC/9.3.0 , foss/2018b |
Bambi¶
Bambi is a high-level Bayesian model-building interface written in Python. It works with the probabilistic programming frameworks PyMC3 and is designed to make it extremely easy to fit Bayesian mixed-effects models common in biology, social sciences and other disciplines.
homepage: https://bambinos.github.io/bambi
version | toolchain |
---|---|
0.7.1 |
foss/2021b , intel/2021b |
bamFilters¶
A utility tool to filter alignments from bam files, using identity percent, low complexity and read coverage.
homepage: https://github.com/institut-de-genomique/bamFilters
version | toolchain |
---|---|
2022-06-30 |
GCC/11.3.0 |
BAMM¶
BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution.
homepage: http://bamm-project.org/
version | toolchain |
---|---|
2.5.0 |
foss/2022a |
BAMSurgeon¶
Tools for adding mutations to existing .bam files, used for testing mutation callers
homepage: https://github.com/adamewing/bamsurgeon
version | versionsuffix | toolchain |
---|---|---|
1.2 |
-Python-2.7.16 |
GCC/8.3.0 |
bamtofastq¶
Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.
homepage: https://github.com/10XGenomics/bamtofastq
version | toolchain |
---|---|
1.4.0 |
GCCcore/10.3.0 |
BamTools¶
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
homepage: https://github.com/pezmaster31/bamtools
version | toolchain |
---|---|
2.4.0 |
foss/2016b |
2.4.1 |
intel/2017a |
2.5.0 |
foss/2016b , intel/2017b |
2.5.1 |
GCC/10.2.0 , GCC/8.2.0-2.31.1 , GCC/8.3.0 , GCC/9.3.0 , foss/2017b , foss/2018a , foss/2018b , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , iccifort/2019.5.281 , iccifort/2020.4.304 , intel/2017b , intel/2018b |
2.5.2 |
GCC/10.3.0 , GCC/11.2.0 , GCC/11.3.0 , GCC/12.2.0 |
BamUtil¶
BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
homepage: http://genome.sph.umich.edu/wiki/BamUtil
version | toolchain |
---|---|
1.0.13 |
intel/2016b |
1.0.14 |
intel/2018a |
Bandage¶
Bandage is a program for visualising de novo assembly graphs
homepage: http://rrwick.github.io/Bandage
version | versionsuffix | toolchain |
---|---|---|
0.8.1 |
_Centos |
system |
0.8.1 |
_Ubuntu |
system |
0.9.0 |
GCCcore/11.2.0 |
barrnap¶
Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes.
homepage: https://github.com/tseemann/barrnap
version | toolchain |
---|---|
0.9 |
GCC/8.2.0-2.31.1 , foss/2018b , gompi/2020b , gompi/2021b |
basemap¶
The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python
homepage: https://matplotlib.org/basemap/
version | versionsuffix | toolchain |
---|---|---|
1.0.7 |
-Python-2.7.13 |
intel/2017a |
1.0.7 |
-Python-3.6.3 |
intel/2017b |
1.0.7 |
-Python-3.6.4 |
intel/2018a |
1.2.0 |
-Python-3.6.6 |
intel/2018b |
1.2.2 |
-Python-3.8.2 |
foss/2020a |
1.3.6 |
foss/2022a |
Bash¶
Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).
homepage: http://www.gnu.org/software/bash
version | toolchain |
---|---|
4.3 |
GCC/4.9.2 |
bashplotlib¶
bashplotlib is a python package and command line tool for making basic plots in the terminal. It's a quick way to visualize data when you don't have a GUI.
homepage: https://github.com/glamp/bashplotlib
version | toolchain |
---|---|
0.6.5 |
GCCcore/10.3.0 |
bat¶
The BAT Python package supports the processing and analysis of Bro data with Pandas, scikit-learn, and Spark
homepage: https://pypi.python.org/pypi/bat
version | versionsuffix | toolchain |
---|---|---|
0.3.3 |
-Python-3.6.3 |
intel/2017b |
batchgenerators¶
Data augmentation toolkit developed at the Division of Medical Image Computing at the German Cancer Research Center (DKFZ) to suit all our deep learning data augmentation needs.
homepage: https://github.com/MIC-DKFZ/batchgenerators
version | toolchain |
---|---|
0.25 |
foss/2021a |
BatMeth2¶
An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.
homepage: https://github.com/GuoliangLi-HZAU/BatMeth2
version | toolchain |
---|---|
2.1 |
foss/2019b |
BayesAss¶
BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes
homepage: http://www.rannala.org/?page_id=245
version | toolchain |
---|---|
3.0.4 |
foss/2016a |
BayesAss3-SNPs¶
Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols.
homepage: https://github.com/stevemussmann/BayesAss3-SNPs
version | toolchain |
---|---|
1.1 |
GCC/11.3.0 |
BayeScan¶
BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
homepage: http://cmpg.unibe.ch/software/BayeScan/
version | toolchain |
---|---|
2.1 |
foss/2016a , foss/2018a , intel/2018a |
BayeScEnv¶
BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation.
homepage: https://github.com/devillemereuil/bayescenv
version | toolchain |
---|---|
1.1 |
GCC/8.3.0 , foss/2016a , iccifort/2019.5.281 |
BayesTraits¶
BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.
homepage: http://www.evolution.reading.ac.uk/BayesTraitsV1.html
version | versionsuffix | toolchain |
---|---|---|
1.0-linux32 |
system |
|
2.0 |
-Beta-Linux64 |
system |
Bazel¶
Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
homepage: https://bazel.io/
version | versionsuffix | toolchain |
---|---|---|
0.4.4 |
system |
|
0.7.0 |
GCCcore/6.4.0 |
|
0.10.0 |
GCCcore/6.4.0 |
|
0.11.0 |
GCCcore/6.4.0 |
|
0.11.1 |
GCCcore/6.4.0 |
|
0.12.0 |
GCCcore/6.4.0 |
|
0.16.0 |
GCCcore/6.4.0 , GCCcore/7.3.0 |
|
0.18.0 |
GCCcore/7.3.0 |
|
0.20.0 |
GCCcore/7.3.0 , GCCcore/8.2.0 |
|
0.25.2 |
GCCcore/8.2.0 |
|
0.26.1 |
GCCcore/8.2.0 , GCCcore/8.3.0 |
|
0.29.1 |
GCCcore/8.2.0 , GCCcore/8.3.0 |
|
0.29.1 |
-Java-1.8 |
GCCcore/9.3.0 |
1.1.0 |
GCCcore/8.3.0 |
|
2.0.0 |
GCCcore/10.2.0 , GCCcore/8.3.0 |
|
3.4.1 |
GCCcore/8.3.0 |
|
3.6.0 |
GCCcore/9.3.0 |
|
3.7.1 |
GCCcore/8.3.0 |
|
3.7.2 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/8.3.0 |
|
4.2.2 |
GCCcore/11.2.0 |
|
5.1.1 |
GCCcore/11.3.0 |
bbcp¶
BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp
homepage: http://www.slac.stanford.edu/~abh/bbcp/
version | versionsuffix | toolchain |
---|---|---|
12.01.30.00.0 |
-amd64_linux26 |
system |
bbFTP¶
bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. bbFTP main features are: * Encoded username and password at connection * SSH and Certificate authentication modules * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression * Automatic retry * Customizable time-outs * Transfer simulation * AFS authentication integration * RFIO interface
homepage: https://software.in2p3.fr/bbftp/
version | toolchain |
---|---|
3.2.1 |
GCCcore/9.3.0 , intel/2016a , system |
BBMap¶
BBMap short read aligner, and other bioinformatic tools.
homepage: https://sourceforge.net/projects/bbmap/
version | versionsuffix | toolchain |
---|---|---|
36.62 |
-Java-1.8.0_112 |
intel/2016b |
37.93 |
foss/2018a , intel/2018a |
|
38.26 |
foss/2018b |
|
38.50b |
GCC/8.2.0-2.31.1 |
|
38.76 |
GCC/8.2.0-2.31.1 |
|
38.79 |
GCC/8.3.0 |
|
38.87 |
iccifort/2020.1.217 |
|
38.90 |
GCC/10.2.0 , GCC/9.3.0 |
|
38.96 |
GCC/10.3.0 |
|
38.98 |
GCC/11.2.0 |
|
39.01 |
GCC/11.3.0 |
bc¶
bc is an arbitrary precision numeric processing language.
homepage: https://www.gnu.org/software/bc/
version | toolchain |
---|---|
1.06.95 |
GCC/4.8.2 |
BCALM¶
de Bruijn graph compaction in low memory
homepage: https://github.com/GATB/bcalm
version | toolchain |
---|---|
2.2.0 |
foss/2018a |
bcbio-gff¶
Read and write Generic Feature Format (GFF) with Biopython integration.
homepage: https://github.com/chapmanb/bcbb/tree/master/gff
version | versionsuffix | toolchain |
---|---|---|
0.6.6 |
-Python-3.8.2 |
foss/2020a |
0.6.7 |
foss/2021a |
|
0.7.0 |
foss/2020b , foss/2022a |
BCEL¶
The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give users a convenient way to analyze, create, and manipulate (binary) Java class files (those ending with .class).
homepage: https://commons.apache.org/proper/commons-bcel/
version | versionsuffix | toolchain |
---|---|---|
5.2 |
-Java-1.8 |
system |
6.5.0 |
-Java-1.8 |
system |
BCFtools¶
Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
homepage: http://www.htslib.org/
version | toolchain |
---|---|
1.3 |
foss/2016a , intel/2016a |
1.3.1 |
foss/2016b |
1.6 |
foss/2016b , foss/2017b , intel/2017b |
1.8 |
GCC/6.4.0-2.28 |
1.9 |
foss/2018a , foss/2018b , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , intel/2018b |
1.10.2 |
GCC/8.3.0 , GCC/9.3.0 , iccifort/2019.5.281 |
1.11 |
GCC/10.2.0 |
1.12 |
GCC/10.2.0 , GCC/10.3.0 , GCC/9.3.0 |
1.14 |
GCC/11.2.0 |
1.15.1 |
GCC/11.3.0 |
1.17 |
GCC/12.2.0 |
bcgTree¶
Automatized phylogenetic tree building from bacterial core genomes.
homepage: https://github.com/molbiodiv/bcgTree
version | versionsuffix | toolchain |
---|---|---|
1.0.10 |
-Perl-5.26.1 |
intel/2018a |
1.1.0 |
-Perl-5.28.0 |
intel/2018b |
bcl-convert¶
The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.
homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html
version | versionsuffix | toolchain |
---|---|---|
4.0.3-2 |
el7.x86_64 |
system |
bcl2fastq2¶
bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
homepage: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
version | versionsuffix | toolchain |
---|---|---|
2.19.1 |
-Python-2.7.12 |
foss/2016b |
2.20.0 |
GCC/10.2.0 , GCC/10.3.0 , GCC/11.2.0 , GCC/11.3.0 , GCC/8.3.0 , GCC/9.3.0 , foss/2018b , intel/2019a |
|
2.20.0 |
-Python-2.7.12 |
foss/2016b |
2.20.0 |
-Python-2.7.14 |
intel/2017b |
bcolz¶
bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes.
homepage: https://bcolz.blosc.org/en/latest/
version | versionsuffix | toolchain |
---|---|---|
1.1.1 |
-Python-2.7.13 |
foss/2017a |
1.2.1 |
foss/2020b |
|
1.2.1 |
-Python-3.8.2 |
foss/2020a |
BDBag¶
The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles.
homepage: https://github.com/fair-research/bdbag
version | versionsuffix | toolchain |
---|---|---|
1.4.1 |
-Python-2.7.14 |
intel/2018a |
1.4.1 |
-Python-3.6.4 |
intel/2018a |
1.6.3 |
intel/2021b |
Beagle¶
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
homepage: https://faculty.washington.edu/browning/beagle/beagle.html
version | versionsuffix | toolchain |
---|---|---|
5.4.22Jul22.46e |
-Java-11 |
system |
beagle-lib¶
beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
homepage: https://github.com/beagle-dev/beagle-lib
version | versionsuffix | toolchain |
---|---|---|
2.1.2 |
foss/2016a , foss/2017a |
|
3.0.1 |
foss/2018a , intel/2018a |
|
3.0.2 |
foss/2018b |
|
3.0.2 |
-CUDA-9.2.88 |
foss/2018b |
3.1.2 |
GCC/10.2.0 , GCC/10.3.0 , GCC/8.2.0-2.31.1 , GCC/9.3.0 , gcccuda/2019b , iccifort/2019.1.144-GCC-8.2.0-2.31.1 |
|
4.0.0 |
GCC/11.3.0 |
Beast¶
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
homepage: https://beast2.org
version | toolchain |
---|---|
1.8.4 |
system |
1.10.1 |
intel/2018a |
1.10.4 |
GCC/10.2.0 , GCC/8.2.0-2.31.1 |
2.4.0 |
foss/2016a |
2.4.7 |
foss/2017a |
2.5.0 |
foss/2018a |
2.5.1 |
foss/2018b |
2.5.2 |
GCC/8.2.0-2.31.1 |
2.6.3 |
gcccuda/2019b |
2.6.4 |
GCC/10.2.0 |
2.6.7 |
GCC/10.3.0 |
2.7.3 |
GCC/11.3.0 |
BeautifulSoup¶
Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.
homepage: https://www.crummy.com/software/BeautifulSoup
version | versionsuffix | toolchain |
---|---|---|
4.6.0 |
-Python-3.6.3 |
intel/2017b |
4.6.3 |
-Python-3.6.4 |
intel/2018a |
4.7.1 |
-Python-3.6.6 |
intel/2018b |
4.8.0 |
GCCcore/8.2.0 |
|
4.9.1 |
GCCcore/8.3.0 |
|
4.9.1 |
-Python-3.8.2 |
GCCcore/9.3.0 |
4.9.3 |
GCCcore/10.2.0 |
|
4.10.0 |
GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 |
|
4.11.1 |
GCCcore/12.2.0 |
BEDOPS¶
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
homepage: http://bedops.readthedocs.io/en/latest/index.html
version | toolchain |
---|---|
2.4.1 |
GCC/4.8.4 |
2.4.2 |
GCC/4.8.2 |
2.4.20 |
system |
2.4.26 |
system |
2.4.30 |
foss/2016b |
2.4.32 |
foss/2018a , intel/2018a |
2.4.35 |
foss/2018b |
2.4.41 |
foss/2021b |
BEDTools¶
BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
homepage: https://bedtools.readthedocs.io/
version | toolchain |
---|---|
2.25.0 |
foss/2016a |
2.26.0 |
GCCcore/6.4.0 , foss/2016a , intel/2016b , intel/2017a , intel/2017b |
2.27.1 |
GCCcore/6.4.0 , foss/2016b , foss/2018b , intel/2017a , intel/2018a |
2.28.0 |
GCC/8.2.0-2.31.1 , foss/2018b , iccifort/2019.1.144-GCC-8.2.0-2.31.1 |
2.29.2 |
GCC/8.3.0 , GCC/9.3.0 |
2.30.0 |
GCC/10.2.0 , GCC/10.3.0 , GCC/11.2.0 , GCC/11.3.0 , GCC/12.2.0 , iccifort/2020.4.304 |
BEEF¶
BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.
homepage: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software
version | toolchain |
---|---|
0.1.1 |
iccifort/2019.5.281 , iccifort/2020.4.304 |
behave¶
behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a software project.
homepage: http://pythonhosted.org/behave
version | versionsuffix | toolchain |
---|---|---|
1.2.5 |
-Python-2.7.12 |
foss/2016b |
1.2.6 |
-Python-3.6.4 |
intel/2018a |
BerkeleyGW¶
The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
homepage: https://www.berkeleygw.org
version | versionsuffix | toolchain |
---|---|---|
1.0.6 |
intel/2016.02-GCC-4.9 |
|
1.1-beta2 |
intel/2016.02-GCC-4.9 |
|
1.2.0 |
intel/2017a , intel/2018a |
|
2.0.0 |
foss/2017b , foss/2018b , intel/2017b , intel/2018a |
|
2.1.0 |
-Python-3.7.4 |
foss/2019b , intel/2019b |
3.0.1 |
foss/2020b , foss/2021a |
BFAST¶
BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: 1) Speed: enables billions of short reads to be mapped quickly. 2) Accuracy: A priori probabilities for mapping reads with defined set of variants. 3) An easy way to measurably tune accuracy at the expense of speed.
homepage: http://bfast.sourceforge.net/
version | toolchain |
---|---|
0.7.0a |
foss/2016b |
BFC¶
BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.
homepage: https://github.com/lh3/bfc
version | toolchain |
---|---|
1 |
foss/2018a |
bgen¶
A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3.
homepage: https://github.com/limix/bgen
version | toolchain |
---|---|
3.0.2 |
GCCcore/7.3.0 |
3.0.3 |
GCCcore/9.3.0 |
4.1.3 |
GCCcore/10.2.0 |
bgen-reader¶
A bgen file format reader. This python package is a wrapper around the bgen library, a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats.
homepage: https://github.com/limix/bgen-reader-py
version | versionsuffix | toolchain |
---|---|---|
3.0.2 |
-Python-3.6.6 |
foss/2018b |
bibtexparser¶
Bibtex parser in Python 2.7 and 3.x
homepage: https://github.com/sciunto-org/python-bibtexparser
version | toolchain |
---|---|
1.1.0 |
GCCcore/8.2.0 |
BiG-SCAPE¶
BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.
homepage: https://bigscape-corason.secondarymetabolites.org/index.html
version | versionsuffix | toolchain |
---|---|---|
1.0.1 |
-Python-3.7.4 |
intel/2019b |
BigDFT¶
BigDFT: electronic structure calculation based on Daubechies wavelets. bigdft-suite is a set of different packages to run bigdft.
homepage: https://gitlab.com/l_sim/bigdft-suite
version | toolchain |
---|---|
1.9.1 |
foss/2021b |
BinSanity¶
BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes.
homepage: https://github.com/edgraham/BinSanity/wiki
version | versionsuffix | toolchain |
---|---|---|
0.3.5 |
-Python-3.7.4 |
foss/2019b |
binutils¶
binutils: GNU binary utilities
homepage: https://directory.fsf.org/project/binutils/
version | toolchain |
---|---|
2.25 |
GCC/4.9.2 , GCC/4.9.2-binutils-2.25 , GCC/4.9.3 , GCC/4.9.3-binutils-2.25 , GCC/5.1.0-binutils-2.25 , GCCcore/4.9.2 , GCCcore/4.9.3 , GCCcore/4.9.4 , system |
2.25.1 |
system |
2.26 |
GCCcore/5.3.0 , GCCcore/5.4.0 , GCCcore/5.5.0 , GCCcore/6.3.0 , system |
2.27 |
GCCcore/6.1.0 , GCCcore/6.2.0 , GCCcore/6.3.0 , system |
2.28 |
GCCcore/6.3.0 , GCCcore/6.4.0 , GCCcore/7.1.0 , system |
2.29 |
GCCcore/7.2.0 , GCCcore/system , system |
2.30 |
GCCcore/7.3.0 , GCCcore/8.1.0 , system |
2.31.1 |
GCCcore/7.4.0 , GCCcore/8.2.0 , system |
2.32 |
GCCcore/8.3.0 , GCCcore/9.1.0 , GCCcore/9.2.0 , system |
2.34 |
GCCcore/10.1.0 , GCCcore/9.3.0 , system |
2.35 |
GCCcore/10.2.0 , system |
2.36.1 |
FCC/4.5.0 , GCCcore/10.3.0 , GCCcore/11.1.0 , GCCcore/8.4.0 , GCCcore/9.4.0 , system |
2.37 |
GCCcore/11.2.0 , system |
2.38 |
GCCcore/11.3.0 , GCCcore/12.1.0 , GCCcore/9.5.0 , system |
2.39 |
GCCcore/12.2.0 , system |
2.40 |
GCCcore/12.3.0 , GCCcore/13.1.0 , system |
Bio-DB-HTS¶
Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
homepage: https://metacpan.org/release/Bio-DB-HTS
version | versionsuffix | toolchain |
---|---|---|
2.11 |
-Perl-5.26.0 |
foss/2017b , intel/2017b |
2.11 |
-Perl-5.26.1 |
intel/2018a |
2.11 |
-Perl-5.28.0 |
foss/2018b |
3.01 |
GCC/10.2.0 , GCC/11.2.0 , GCC/11.3.0 |
|
3.01 |
-Perl-5.28.1 |
GCC/8.2.0-2.31.1 |
Bio-EUtilities¶
BioPerl low-level API for retrieving and storing data from NCBI eUtils
homepage: https://github.com/bioperl/bio-eutilities
version | toolchain |
---|---|
1.76 |
GCCcore/8.3.0 |
Bio-SamTools¶
This is a Perl interface to the SAMtools sequence alignment interface.
homepage: http://search.cpan.org/~lds/Bio-SamTools/
version | versionsuffix | toolchain |
---|---|---|
1.43 |
-Perl-5.24.1 |
intel/2017a |
Bio-SearchIO-hmmer¶
Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org.
homepage: https://metacpan.org/pod/Bio::SearchIO::hmmer3
version | toolchain |
---|---|
1.7.3 |
GCC/10.2.0 , GCC/10.3.0 , GCC/11.2.0 , GCC/11.3.0 |
bioawk¶
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
homepage: https://github.com/lh3/bioawk
version | toolchain |
---|---|
1.0 |
GCC/10.3.0 , GCC/11.2.0 , foss/2018b |
biobambam2¶
Tools for processing BAM files
homepage: https://github.com/gt1/biobambam2
version | toolchain |
---|---|
2.0.87 |
GCC/11.3.0 , intel/2018a |
biogeme¶
Biogeme is a open source Python package designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models.
homepage: https://pypi.python.org/pypi/biogeme
version | toolchain |
---|---|
3.1.2 |
foss/2021a |
3.2.6 |
foss/2022a |
3.2.8 |
foss/2021a |
3.2.10 |
foss/2022a |
biom-format¶
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
homepage: https://biom-format.org
version | versionsuffix | toolchain |
---|---|---|
2.1.10 |
-Python-3.8.2 |
foss/2020a |
2.1.12 |
foss/2021b |
|
2.1.14 |
foss/2022a |
biomart-perl¶
The BioMart Perl API allows you to go a step further with BioMart and integrate BioMart Perl Code into custom Perl scripts.
homepage: https://useast.ensembl.org/info/data/biomart/biomart_perl_api.html
version | versionsuffix | toolchain |
---|---|---|
0.7_e6db561 |
-Perl-5.26.0 |
GCCcore/6.4.0 |
BioPerl¶
Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
homepage: https://bioperl.org/
version | versionsuffix | toolchain |
---|---|---|
1.6.924 |
-Perl-5.20.3 |
intel/2016a |
1.6.924 |
-Perl-5.22.1 |
foss/2016a |
1.7.0 |
-Perl-5.24.0 |
foss/2016b |
1.7.1 |
-Perl-5.24.0 |
intel/2016b |
1.7.1 |
-Perl-5.24.1 |
intel/2017a |
1.7.2 |
GCCcore/8.3.0 |
|
1.7.2 |
-Perl-5.26.0 |
foss/2017b , intel/2017b |
1.7.2 |
-Perl-5.26.1 |
intel/2018a |
1.7.2 |
-Perl-5.28.0 |
foss/2018b , intel/2018b |
1.7.2 |
-Perl-5.28.1 |
GCCcore/8.2.0 |
1.7.7 |
GCCcore/9.3.0 |
|
1.7.8 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 |
BioPP¶
Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.
homepage: https://github.com/BioPP/bpp-core
version | toolchain |
---|---|
2.4.1 |
GCC/8.2.0-2.31.1 , GCC/9.3.0 |
Biopython¶
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
homepage: https://www.biopython.org
version | versionsuffix | toolchain |
---|---|---|
1.65 |
-Python-2.7.11 |
foss/2016a |
1.68 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
1.68 |
-Python-3.5.2 |
foss/2016b , intel/2016b |
1.70 |
-Python-2.7.13 |
foss/2017a |
1.70 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
1.70 |
-Python-3.6.1 |
intel/2017a |
1.70 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
1.71 |
-Python-2.7.14 |
intel/2018a |
1.71 |
-Python-3.6.4 |
foss/2018a , intel/2018a |
1.72 |
-Python-2.7.15 |
foss/2018b , intel/2018b |
1.72 |
-Python-3.6.6 |
foss/2018b |
1.73 |
foss/2019a , fosscuda/2019a , intel/2019a |
|
1.73 |
-Python-3.6.6 |
foss/2018b |
1.74 |
foss/2019a |
|
1.75 |
-Python-2.7.16 |
foss/2019b |
1.75 |
-Python-3.7.4 |
foss/2019b , fosscuda/2019b , intel/2019b |
1.76 |
-Python-2.7.18 |
foss/2020b |
1.78 |
foss/2020b , fosscuda/2020b , intel/2020b |
|
1.78 |
-Python-3.8.2 |
foss/2020a , intel/2020a |
1.79 |
foss/2021a , foss/2021b , foss/2022a , intel/2021b |
|
1.81 |
foss/2022b |
BioServices¶
Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).
homepage: https://bioservices.readthedocs.io/
version | versionsuffix | toolchain |
---|---|---|
1.7.9 |
-Python-3.8.2 |
foss/2020a |
BirdNET¶
BirdNET is a research platform that aims at recognizing birds by sound at scale. We support various hardware and operating systems such as Arduino microcontrollers, the Raspberry Pi, smartphones, web browsers, workstation PCs, and even cloud services. BirdNET is a citizen science platform as well as an analysis software for extremely large collections of audio. BirdNET aims to provide innovative tools for conservationists, biologists, and birders alike.
homepage: https://birdnet.cornell.edu/
version | versionsuffix | toolchain |
---|---|---|
20201214 |
-Python-3.7.4 |
fosscuda/2019b |
biscuit¶
Utilities to help analyze bisulfite-treated sequence data
homepage: https://github.com/zwdzwd/biscuit
version | toolchain |
---|---|
0.1.4 |
foss/2016a |
Bismark¶
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
homepage: https://www.bioinformatics.babraham.ac.uk/projects/bismark/
version | toolchain |
---|---|
0.19.0 |
intel/2017b |
0.20.1 |
foss/2018b , intel/2018b |
0.23.1 |
foss/2021b |
0.24.0 |
GCC/11.3.0 |
Bison¶
Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
homepage: https://www.gnu.org/software/bison
version | toolchain |
---|---|
2.7 |
GCC/4.8.1 , GCC/4.8.4 , GCCcore/6.3.0 , GCCcore/6.4.0 , system |
3.0.2 |
GCC/4.8.2 |
3.0.3 |
GCC/4.9.2 |
3.0.4 |
GCC/4.9.2 , GCC/4.9.2-binutils-2.25 , GCC/4.9.3 , GCC/4.9.3-2.25 , GCC/4.9.3-binutils-2.25 , GCC/5.1.0-binutils-2.25 , GCCcore/4.9.2 , GCCcore/4.9.3 , GCCcore/4.9.4 , GCCcore/5.3.0 , GCCcore/5.4.0 , GCCcore/5.5.0 , GCCcore/6.1.0 , GCCcore/6.2.0 , GCCcore/6.3.0 , GCCcore/6.4.0 , GCCcore/7.1.0 , GCCcore/7.2.0 , GCCcore/7.3.0 , GCCcore/8.1.0 , GCCcore/system , GNU/4.9.3-2.25 , foss/2016a , foss/2016b , gimkl/2.11.5 , gimkl/2017a , intel/2016.02-GCC-4.9 , intel/2016a , intel/2016b , iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 , system |
3.0.5 |
GCCcore/5.5.0 , GCCcore/6.3.0 , GCCcore/6.4.0 , GCCcore/7.2.0 , GCCcore/7.3.0 , GCCcore/8.1.0 , GCCcore/8.2.0 , GCCcore/system , system |
3.2.2 |
GCCcore/7.4.0 |
3.3.2 |
GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/8.4.0 , GCCcore/9.1.0 , GCCcore/9.2.0 , system |
3.5.2 |
system |
3.5.3 |
GCCcore/10.2.0 , GCCcore/9.3.0 , system |
3.6.1 |
GCCcore/10.1.0 |
3.7.1 |
GCCcore/10.2.0 , system |
3.7.6 |
FCC/4.5.0 , GCCcore/10.3.0 , GCCcore/11.1.0 , GCCcore/11.2.0 , GCCcore/9.4.0 , system |
3.8.2 |
GCCcore/11.3.0 , GCCcore/12.1.0 , GCCcore/12.2.0 , GCCcore/12.3.0 , GCCcore/13.1.0 , GCCcore/9.5.0 , system |
bitarray¶
bitarray provides an object type which efficiently represents an array of booleans
homepage: https://github.com/ilanschnell/bitarray
version | versionsuffix | toolchain |
---|---|---|
0.8.3 |
-Python-2.7.15 |
intel/2018b |
0.8.3 |
-Python-3.6.6 |
intel/2018b |
1.2.1 |
-Python-3.7.4 |
foss/2019b |
1.5.3 |
-Python-2.7.16 |
GCC/8.3.0 |
BLACS¶
The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.
homepage: http://www.netlib.org/blacs/
version | toolchain |
---|---|
1.1 |
gmvapich2/2016a |
BLASR¶
The PacBio® long read aligner
homepage: https://github.com/PacificBiosciences/blasr
version | toolchain |
---|---|
2.2 |
intel/2016b |
5.3.3 |
gompi/2019a |
20170330 |
intel/2017a |
blasr_libcpp¶
Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences
homepage: https://github.com/PacificBiosciences/blasr_libcpp
version | toolchain |
---|---|
20170426 |
intel/2017a |
BLAST¶
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
homepage: http://blast.ncbi.nlm.nih.gov/
version | versionsuffix | toolchain |
---|---|---|
2.2.26 |
-Linux_x86_64 |
system |
2.8.1 |
-Linux_x86_64 |
system |
2.10.0 |
-Linux_x86_64 |
system |
2.10.1 |
-Linux_x86_64 |
system |
2.11.0 |
-Linux_x86_64 |
system |
BLAST+¶
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
homepage: https://blast.ncbi.nlm.nih.gov/
version | versionsuffix | toolchain |
---|---|---|
2.2.31 |
system |
|
2.3.0 |
-Python-2.7.11 |
foss/2016a |
2.6.0 |
-Python-2.7.12 |
foss/2016b |
2.6.0 |
-Python-2.7.13 |
foss/2017a , intel/2017a |
2.6.0 |
-Python-2.7.14 |
intel/2017b |
2.7.1 |
foss/2018a , foss/2018b , intel/2018a , intel/2018b |
|
2.7.1 |
-Python-2.7.14 |
intel/2017b |
2.8.1 |
foss/2018b |
|
2.9.0 |
gompi/2019a , gompi/2019b , gompi/2021b , iimpi/2019a , iimpi/2019b |
|
2.10.1 |
gompi/2020a , iimpi/2020a |
|
2.11.0 |
gompi/2019b , gompi/2020a , gompi/2020b , gompi/2021a |
|
2.12.0 |
gompi/2021b |
|
2.13.0 |
gompi/2022a |
BLAT¶
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
homepage: https://genome.ucsc.edu/goldenPath/help/blatSpec.html
version | toolchain |
---|---|
3.5 |
GCC/8.2.0-2.31.1 , GCC/8.3.0 , GCC/9.3.0 , foss/2016b , foss/2018b , intel/2016b , intel/2017a |
3.7 |
GCC/11.3.0 |
Blender¶
Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
homepage: https://www.blender.org/
version | versionsuffix | toolchain |
---|---|---|
2.77a |
-Python-3.5.2 |
intel/2016b |
2.79 |
-Python-3.6.1 |
intel/2017a |
2.79b |
-Python-3.6.6 |
intel/2018b |
2.79b |
-Python-3.6.6-CUDA-9.2.88 |
foss/2018b |
2.81 |
-Python-3.7.4 |
foss/2019b , intel/2019b |
3.0.0 |
-linux-x64 |
system |
3.1.2 |
-linux-x64 |
system |
3.2.2 |
-linux-x64 |
system |
3.3.1 |
-linux-x86_64-CUDA-11.7.0 |
system |
3.4.1 |
-linux-x86_64-CUDA-11.7.0 |
system |
3.5.0 |
-linux-x86_64-CUDA-11.7.0 |
system |
BLIS¶
AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
homepage: https://developer.amd.com/amd-cpu-libraries/blas-library/
version | versionsuffix | toolchain |
---|---|---|
0.3.2 |
GCC/7.3.0-2.30 |
|
0.6.0 |
GCC/8.3.0-2.32 |
|
0.8.0 |
GCCcore/10.2.0 , GCCcore/9.3.0 |
|
0.8.1 |
GCC/10.3.0 , GCC/11.2.0 , GCCcore/10.3.0 |
|
0.9.0 |
GCC/11.3.0 , GCC/12.2.0 , intel-compilers/2022.1.0 |
|
1.2 |
-amd |
GCC/7.3.0-2.30 |
2.2 |
-amd |
GCCcore/9.3.0 |
3.0 |
-amd |
GCCcore/10.3.0 |
3.0.1 |
-amd |
GCC/11.2.0 , GCCcore/10.2.0 , GCCcore/10.3.0 |
3.1 |
-amd |
GCCcore/11.2.0 |
Blitz++¶
Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
homepage: https://github.com/blitzpp/blitz
version | toolchain |
---|---|
0.10 |
GCCcore/6.4.0 , foss/2016a |
1.0.2 |
GCCcore/10.2.0 , GCCcore/11.3.0 , GCCcore/12.2.0 , GCCcore/12.3.0 , GCCcore/9.3.0 |
BlobTools¶
A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.
homepage: https://blobtools.readme.io/docs
version | versionsuffix | toolchain |
---|---|---|
20180528 |
-Python-2.7.15 |
foss/2018b |
Block¶
Block implements the density matrix renormalization group (DMRG) algorithm for quantum chemistry.
homepage: https://sanshar.github.io/Block/
version | toolchain |
---|---|
1.5.3-20200525 |
foss/2022a |
Blosc¶
Blosc, an extremely fast, multi-threaded, meta-compressor library
homepage: https://www.blosc.org/
version | toolchain |
---|---|
1.11.1 |
intel/2016b |
1.12.1 |
GCCcore/6.4.0 , foss/2016b , foss/2017a , intel/2017a |
1.14.2 |
GCCcore/6.4.0 , foss/2016a |
1.14.4 |
GCCcore/7.3.0 |
1.17.0 |
GCCcore/8.2.0 |
1.17.1 |
GCCcore/8.3.0 , GCCcore/9.3.0 |
1.21.0 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
1.21.1 |
GCCcore/11.2.0 |
1.21.3 |
GCCcore/11.3.0 , GCCcore/12.2.0 |
Blosc2¶
Blosc, an extremely fast, multi-threaded, meta-compressor library
homepage: https://www.blosc.org/
version | toolchain |
---|---|
2.0.3 |
GCCcore/10.2.0 |
2.0.4 |
GCCcore/10.3.0 |
2.4.3 |
GCCcore/11.3.0 |
2.6.1 |
GCCcore/11.3.0 |
2.8.0 |
GCCcore/12.2.0 |
BLT¶
BLT is an extension to the Tk toolkit, adding new widgets, geometry managers, and miscellaneous commands.
homepage: http://blt.sourceforge.net/
version | toolchain |
---|---|
20181223 |
GCCcore/11.2.0 |
bmtagger¶
Best Match Tagger for removing human reads from metagenomics datasets
homepage: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/
version | toolchain |
---|---|
3.101 |
foss/2018b , gompi/2019a , gompi/2020b |
bnpy¶
Bayesian nonparametric machine learning for python provides code for training popular clustering models on large datasets. The focus is on Bayesian nonparametric models based on the Dirichlet process, but it also provides parametric counterparts.
homepage: https://github.com/bnpy/bnpy
version | versionsuffix | toolchain |
---|---|---|
0.1.6 |
-Python-2.7.15 |
foss/2018b |
BOINC¶
BOINC is a program that lets you donate your idle computer time to science projects like SETI@home, Climateprediction.net, Rosetta@home, World Community Grid, and many others.
homepage: https://boinc.berkeley.edu
version | versionsuffix | toolchain |
---|---|---|
7.2.42 |
-client |
GCC/4.8.2 |
bokeh¶
Statistical and novel interactive HTML plots for Python
homepage: https://github.com/bokeh/bokeh
version | versionsuffix | toolchain |
---|---|---|
0.12.3 |
-Python-2.7.12 |
intel/2016b |
0.12.3 |
-Python-3.5.2 |
intel/2016b |
0.12.15 |
-Python-3.6.4 |
intel/2018a |
1.0.4 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
1.3.4 |
-Python-3.7.2 |
foss/2019a |
1.4.0 |
-Python-3.7.4 |
foss/2019b , fosscuda/2019b , intel/2019b |
2.0.2 |
-Python-3.8.2 |
foss/2020a , intel/2020a |
2.2.3 |
foss/2020b , fosscuda/2020b , intel/2020b , intelcuda/2020b |
|
2.4.1 |
foss/2021a |
|
2.4.2 |
foss/2021b |
|
2.4.3 |
foss/2022a |
BoltzTraP¶
Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients.
homepage: http://www.icams.de/content/departments/cmat/boltztrap/
version | toolchain |
---|---|
1.2.5 |
intel/2016a |
BoltzTraP2¶
BoltzTraP2 provides a numerically stable and efficient method for obtaining analytic representations of electronic bands based on density-functional-theory results for relatively sparse grids. It achieves this goal by using smoothed Fourier interpolation.
homepage: https://www.boltztrap.org
version | toolchain |
---|---|
22.12.1 |
foss/2022a |
Bonito¶
Convolution Basecaller for Oxford Nanopore Reads
homepage: https://github.com/nanoporetech/bonito
version | versionsuffix | toolchain |
---|---|---|
0.1.0 |
-Python-3.7.4 |
foss/2019b , fosscuda/2019b |
0.1.4 |
-Python-3.7.4 |
fosscuda/2019b |
0.2.0 |
-Python-3.7.4 |
fosscuda/2019b |
0.2.2 |
-Python-3.7.4 |
fosscuda/2019b |
0.3.2 |
-Python-3.7.4 |
fosscuda/2019b |
0.3.5 |
-Python-3.7.4 |
fosscuda/2019b |
0.3.8 |
fosscuda/2020b |
|
0.4.0 |
fosscuda/2020b |
Bonmin¶
Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.
homepage: https://coin-or.github.io/Ipopt
version | toolchain |
---|---|
1.8.7 |
intel/2019a |
Bonnie++¶
Enhanced performance Test of Filesystem I/O
homepage: https://www.coker.com.au/bonnie++
version | toolchain |
---|---|
1.97 |
foss/2016a |
2.00a |
GCC/10.3.0 |
Boost¶
Boost provides free peer-reviewed portable C++ source libraries.
homepage: https://www.boost.org/
version | versionsuffix | toolchain |
---|---|---|
1.54.0 |
-Python-2.7.12 |
foss/2016b |
1.55.0 |
system |
|
1.55.0 |
-Python-2.7.11 |
foss/2016a |
1.57.0 |
-Python-2.7.10 |
gimkl/2.11.5 |
1.58.0 |
intel/2017a |
|
1.58.0 |
-Python-2.7.11 |
foss/2016a , intel/2016a |
1.58.0 |
-serial |
GCC/4.9.2 |
1.59.0 |
-Python-2.7.11 |
foss/2016a , intel/2016a |
1.60.0 |
foss/2016a , intel/2016a |
|
1.60.0 |
-Python-2.7.11 |
foss/2016a , intel/2016a |
1.60.0 |
-Python-3.5.1 |
foss/2016a |
1.61.0 |
foss/2016a , foss/2016b , intel/2016a , intel/2016b |
|
1.61.0 |
-Python-2.7.11 |
foss/2016a , intel/2016a |
1.61.0 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
1.61.0 |
-Python-3.5.1 |
foss/2016a |
1.62.0 |
-Python-2.7.12 |
intel/2016b |
1.63.0 |
foss/2017a |
|
1.63.0 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
1.63.0 |
-Python-2.7.13 |
foss/2017a , intel/2017a |
1.63.0 |
-Python-2.7.14 |
foss/2018a , intel/2017b |
1.63.0 |
-Python-3.5.2 |
foss/2016b |
1.64.0 |
gompi/2019a , gompic/2019a , intel/2017a |
|
1.64.0 |
-Python-2.7.13 |
intel/2017a |
1.65.0 |
-Python-2.7.13 |
intel/2017a |
1.65.1 |
foss/2017a , foss/2017b , intel/2017a , intel/2017b |
|
1.65.1 |
-Python-2.7.13 |
intel/2017a |
1.65.1 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
1.65.1 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
1.66.0 |
foss/2018a , intel/2017b , intel/2018.01 , intel/2018a |
|
1.66.0 |
-Python-2.7.14 |
foss/2018a , intel/2017b , intel/2018a |
1.66.0 |
-Python-3.6.3 |
intel/2018.01 |
1.66.0 |
-Python-3.6.4 |
foss/2018a , intel/2018a |
1.66.0 |
-no_mpi |
GCCcore/6.4.0 |
1.67.0 |
foss/2018b , fosscuda/2018b , intel/2018a , intel/2018b |
|
1.67.0 |
-Python-2.7.14 |
foss/2018a |
1.68.0 |
-Python-2.7.15 |
foss/2018b , intel/2018b |
1.68.0 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
1.69.0 |
intel/2019.01 |
|
1.70.0 |
gompi/2019a , gompic/2019a , iimpi/2019a , iimpic/2019a |
|
1.71.0 |
gompi/2019b , gompic/2019b , iimpi/2019b , iimpic/2019b |
|
1.72.0 |
gompi/2020a , gompic/2020a , iimpi/2020a |
|
1.72.0 |
-no_mpi |
GCCcore/9.3.0 |
1.74.0 |
GCC/10.2.0 , iccifort/2020.4.304 |
|
1.75.0 |
GCC/11.2.0 |
|
1.76.0 |
GCC/10.3.0 , intel-compilers/2021.2.0 |
|
1.77.0 |
GCC/11.2.0 , intel-compilers/2021.4.0 |
|
1.79.0 |
GCC/11.2.0 , GCC/11.3.0 |
|
1.81.0 |
GCC/12.2.0 |
Boost.MPI¶
Boost provides free peer-reviewed portable C++ source libraries.
homepage: https://www.boost.org/
version | toolchain |
---|---|
1.76.0 |
gompi/2021a |
1.77.0 |
gompi/2021b |
1.79.0 |
gompi/2022a |
Boost.Python¶
Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
homepage: https://boostorg.github.io/python
version | versionsuffix | toolchain |
---|---|---|
1.64.0 |
gompi/2019a , gompic/2019a |
|
1.65.1 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
1.66.0 |
-Python-2.7.14 |
intel/2018a |
1.66.0 |
-Python-3.6.4 |
foss/2018a , intel/2018a |
1.67.0 |
-Python-2.7.15 |
foss/2018b , fosscuda/2018b , intel/2018b |
1.67.0 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
1.70.0 |
gompi/2019a , gompic/2019a , iimpi/2019a , iimpic/2019a |
|
1.71.0 |
gompi/2019b , gompic/2019b , iimpi/2019b , iimpic/2019b |
|
1.72.0 |
gompi/2020a , gompic/2020a , iimpi/2020a |
|
1.74.0 |
GCC/10.2.0 |
|
1.76.0 |
GCC/10.3.0 |
|
1.77.0 |
GCC/11.2.0 |
|
1.79.0 |
GCC/11.3.0 |
boost_histogram¶
Boost-histogram is a Python package providing Python bindings for Boost.Histogram.
homepage: https://boost-histogram.readthedocs.io
version | toolchain |
---|---|
1.2.1 |
foss/2021a |
boto3¶
Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python, which allows Python developers to write software that makes use of services like Amazon S3 and Amazon EC2.
homepage: https://github.com/boto/boto3
version | toolchain |
---|---|
1.20.13 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
1.26.37 |
GCCcore/11.3.0 |
Bottleneck¶
Fast NumPy array functions written in C
homepage: https://kwgoodman.github.io/bottleneck-doc
version | versionsuffix | toolchain |
---|---|---|
1.2.1 |
-Python-3.6.4 |
intel/2018a |
1.3.2 |
-Python-3.8.2 |
foss/2020a |
1.3.6 |
foss/2022a |
|
1.3.7 |
foss/2022a |
Bowtie¶
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
version | toolchain |
---|---|
1.1.2 |
GCCcore/5.4.0 , GCCcore/6.3.0 , foss/2016a , intel/2016b , intel/2017a , intel/2018a |
1.2.1.1 |
foss/2016b , intel/2017b |
1.2.2 |
foss/2018b , intel/2017b , intel/2018a |
1.2.3 |
GCC/8.2.0-2.31.1 , GCC/8.3.0 , GCC/9.3.0 , foss/2018b , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , iccifort/2019.5.281 |
1.3.0 |
GCC/10.2.0 , GCC/9.3.0 |
1.3.1 |
GCC/11.2.0 , GCC/11.3.0 |
Bowtie2¶
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
homepage: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
version | toolchain |
---|---|
2.2.8 |
foss/2016a |
2.2.9 |
foss/2016a , intel/2016b |
2.3.2 |
foss/2016b , foss/2017a , intel/2017a |
2.3.3.1 |
intel/2017b |
2.3.4 |
intel/2017b |
2.3.4.1 |
foss/2017b , intel/2017b , intel/2018a |
2.3.4.2 |
foss/2018b , intel/2018b |
2.3.4.3 |
foss/2017b |
2.3.5.1 |
GCC/8.2.0-2.31.1 , GCC/8.3.0 , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , iccifort/2019.5.281 |
2.4.1 |
GCC/9.3.0 |
2.4.2 |
GCC/10.2.0 , GCC/9.3.0 |
2.4.4 |
GCC/10.3.0 , GCC/11.2.0 |
2.4.5 |
GCC/11.3.0 |
Bpipe¶
Bpipe - a tool for running and managing bioinformatics pipelines
homepage: http://docs.bpipe.org/
version | toolchain |
---|---|
0.9.9.2 |
intel/2017a |
bpp¶
The aim of this project is to implement a versatile high-performance version of the BPP software.
homepage: https://github.com/bpp/bpp
version | toolchain |
---|---|
4.3.8 |
GCC/8.3.0 |
4.4.0 |
GCC/10.3.0 |
bpytop¶
Resource monitor that shows usage and stats for processor, memory, disks, network and processes.
homepage: https://github.com/aristocratos/bpytop/
version | toolchain |
---|---|
1.0.60 |
GCCcore/10.2.0 |
1.0.67 |
GCCcore/10.3.0 |
Bracken¶
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length.
homepage: https://ccb.jhu.edu/software/bracken/
version | toolchain |
---|---|
2.6.0 |
GCCcore/9.3.0 |
2.6.2 |
GCCcore/11.2.0 |
2.7 |
GCCcore/11.2.0 |
Braindecode¶
Braindecode is an open-source Python toolbox for decoding raw electrophysiological brain data with deep learning models. It includes dataset fetchers, data preprocessing and visualization tools, as well as implementations of several deep learning architectures and data augmentations for analysis of EEG, ECoG and MEG.
homepage: https://braindecode.org/
version | versionsuffix | toolchain |
---|---|---|
0.7 |
-PyTorch-1.10.0 |
foss/2021a |
0.7 |
-PyTorch-1.10.0-CUDA-11.3.1 |
foss/2021a |
BRAKER¶
BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.
homepage: https://github.com/Gaius-Augustus/BRAKER
version | versionsuffix | toolchain |
---|---|---|
2.1.2 |
intel/2019a |
|
2.1.5 |
-Python-3.7.4 |
intel/2019b |
2.1.6 |
foss/2021b , foss/2022a |
BreakDancer¶
BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads
homepage: http://gmt.genome.wustl.edu/packages/breakdancer
version | toolchain |
---|---|
1.4.5 |
intel/2017a |
breseq¶
breseq is a computational pipeline for the analysis of short-read re-sequencing data
homepage: https://barricklab.org/breseq
version | versionsuffix | toolchain |
---|---|---|
0.35.0 |
-R-3.6.0 |
intel/2019a |
0.35.4 |
-R-4.0.0 |
foss/2020a |
0.36.1 |
foss/2021b |
|
0.38.1 |
foss/2022a |
Brotli¶
Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.
homepage: https://github.com/google/brotli
version | toolchain |
---|---|
1.0.9 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/12.2.0 , GCCcore/12.3.0 , GCCcore/8.3.0 |
Brotli-python¶
Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.
homepage: https://github.com/google/brotli
version | toolchain |
---|---|
1.0.9 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.3.0 , GCCcore/12.2.0 |
Brunsli¶
Brunsli is a lossless JPEG repacking library.
homepage: https://github.com/google/brunsli/
version | toolchain |
---|---|
0.1 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.3.0 , GCCcore/12.2.0 , GCCcore/12.3.0 |
bsddb3¶
bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects.
homepage: https://pypi.org/project/bsddb3/
version | versionsuffix | toolchain |
---|---|---|
6.2.6 |
GCCcore/8.2.0 |
|
6.2.6 |
-Python-2.7.15 |
fosscuda/2018b |
6.2.9 |
GCCcore/10.2.0 , GCCcore/11.3.0 |
BSMAPz¶
Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study.
homepage: https://github.com/zyndagj/BSMAPz
version | versionsuffix | toolchain |
---|---|---|
1.1.1 |
-Python-2.7.16 |
intel/2019b |
Bsoft¶
Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages.
homepage: https://lsbr.niams.nih.gov/bsoft/
version | toolchain |
---|---|
2.0.2 |
foss/2017b |
2.0.7 |
GCC/9.3.0 |
BSseeker2¶
BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.
homepage: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2
version | versionsuffix | toolchain |
---|---|---|
2.1.8 |
-Python-2.7.16 |
GCC/8.3.0 , iccifort/2019.5.281 |
BuDDy¶
A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much more.
homepage: http://buddy.sourceforge.net/
version | toolchain |
---|---|
2.4 |
GCCcore/10.2.0 |
BUFRLIB¶
NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself.
homepage: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB
version | toolchain |
---|---|
11.3.0.2 |
iccifort/2020.1.217 |
build¶
A simple, correct Python build frontend.
homepage: https://github.com/pypa/build
version | toolchain |
---|---|
0.10.0 |
foss/2022a |
buildenv¶
This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show
homepage:
version | versionsuffix | toolchain |
---|---|---|
default |
FCC/4.5.0 , Fujitsu/21.05 , foss/2017b , foss/2018b , foss/2019b , foss/2020a , foss/2020b , foss/2021a , foss/2021b , foss/2022a , foss/2022b , fosscuda/2019b , fosscuda/2020a , fosscuda/2020b , intel/2016b , intel/2017a , intel/2019b , intel/2020a , intel/2020b , intel/2021a , intel/2021b , intel/2022a , intel/2022b , intelcuda/2019b , intelcuda/2020a , intelcuda/2020b |
|
default |
-CUDA-11.3.1 |
foss/2021a |
default |
-CUDA-11.4.1 |
foss/2021b |
default |
-CUDA-11.7.0 |
foss/2022a |
default |
-CUDA-12.0.0 |
foss/2022b |
buildingspy¶
Python modules for automating Modelica simulations and for running unit test for the Buildings library
homepage: https://simulationresearch.lbl.gov/modelica/buildingspy
version | toolchain |
---|---|
4.0.0 |
foss/2022a |
Bullet¶
Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics.
homepage: http://bulletphysics.org/
version | toolchain |
---|---|
2.83.7 |
foss/2016a , intel/2016a |
BUSCO¶
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
homepage: https://busco.ezlab.org/
version | versionsuffix | toolchain |
---|---|---|
1.22 |
-Python-2.7.13 |
intel/2017a |
2.0.1 |
-Python-2.7.13 |
intel/2017a |
3.0.2 |
-Python-2.7.15 |
intel/2018b |
4.0.5 |
-Python-3.7.4 |
foss/2019b |
4.0.6 |
foss/2020b |
|
5.0.0 |
foss/2020b |
|
5.1.2 |
foss/2020b |
|
5.4.2 |
foss/2021a |
|
5.4.3 |
foss/2021b |
|
5.4.5 |
foss/2022a |
BUStools¶
bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.
homepage: https://github.com/BUStools/bustools
version | toolchain |
---|---|
0.40.0 |
GCCcore/9.3.0 , foss/2018b |
BWA¶
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
homepage: http://bio-bwa.sourceforge.net/
version | toolchain |
---|---|
0.7.12 |
foss/2016b |
0.7.13 |
foss/2016a , intel/2016a |
0.7.15 |
GCCcore/5.4.0 , GCCcore/6.4.0 , foss/2016a , foss/2016b , intel/2016b , intel/2017a |
0.7.16a |
foss/2016b , intel/2017a |
0.7.17 |
GCC/10.2.0 , GCC/10.3.0 , GCC/8.2.0-2.31.1 , GCC/8.3.0 , GCC/9.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/12.2.0 , foss/2017b , foss/2018a , foss/2018b , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , iccifort/2019.5.281 , iccifort/2020.4.304 , intel/2017b , intel/2018a , intel/2018b |
bwa-meth¶
Fast and accurante alignment of BS-Seq reads.
homepage: https://github.com/brentp/bwa-meth
version | toolchain |
---|---|
0.2.2 |
iccifort/2019.1.144-GCC-8.2.0-2.31.1 , iccifort/2019.5.281 |
0.2.6 |
GCC/11.3.0 |
bwakit¶
Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.
homepage: https://github.com/lh3/bwa/tree/master/bwakit
version | versionsuffix | toolchain |
---|---|---|
0.7.15 |
_x64-linux |
system |
bwidget¶
The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.
homepage: https://core.tcl-lang.org/bwidget/home
version | toolchain |
---|---|
1.9.13 |
GCCcore/8.2.0 |
1.9.14 |
GCCcore/10.2.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
1.9.15 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
BWISE¶
de Bruijn Workflow using Integral information of Short pair End reads
homepage: https://github.com/Malfoy/BWISE
version | versionsuffix | toolchain |
---|---|---|
20180820 |
-Python-3.6.4 |
foss/2018a |
bx-python¶
The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
homepage: https://github.com/bxlab/bx-python
version | versionsuffix | toolchain |
---|---|---|
0.7.4 |
-Python-2.7.12 |
foss/2016b |
0.7.4 |
-Python-2.7.13 |
intel/2017a |
0.8.1 |
-Python-2.7.14 |
intel/2018a |
0.8.2 |
-Python-3.6.6 |
foss/2018b |
0.8.4 |
foss/2019a |
|
0.8.8 |
-Python-3.7.4 |
foss/2019b |
0.8.9 |
-Python-3.8.2 |
foss/2020a |
0.8.11 |
foss/2021a |
|
0.8.13 |
foss/2021b |
|
0.9.0 |
foss/2022a |
BXH_XCEDE_TOOLS¶
A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.
homepage: http://www.nitrc.org/projects/bxh_xcede_tools/
version | toolchain |
---|---|
1.11.1 |
system |
byacc¶
Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.
homepage: http://invisible-island.net/byacc/byacc.html
version | toolchain |
---|---|
20160324 |
intel/2016a |
20160606 |
foss/2016b , intel/2016b |
20170709 |
GCCcore/6.4.0 |
byobu¶
Byobu is an elegant enhancement of the otherwise functional, plain, practical GNU Screen. Byobu includes an enhanced profile, configuration utilities, and system status notifications for the GNU screen window manager as well as the Tmux terminal multiplexer
homepage: https://byobu.org
version | toolchain |
---|---|
5.133 |
GCC/8.3.0 |
bzip2¶
bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
homepage: https://sourceware.org/bzip2
version | toolchain |
---|---|
1.0.6 |
GCC/4.8.1 , GCC/4.8.2 , GCC/4.8.4 , GCC/4.9.2 , GCC/4.9.3-2.25 , GCC/5.4.0-2.26 , GCCcore/4.9.3 , GCCcore/5.4.0 , GCCcore/6.3.0 , GCCcore/6.4.0 , GCCcore/7.2.0 , GCCcore/7.3.0 , GCCcore/8.2.0 , GNU/4.9.3-2.25 , foss/2016.04 , foss/2016a , foss/2016b , gimkl/2.11.5 , gimkl/2017a , intel/2016.02-GCC-4.9 , intel/2016a , intel/2016b , iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 , system |
1.0.8 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/12.2.0 , GCCcore/12.3.0 , GCCcore/13.1.0 , GCCcore/8.3.0 , GCCcore/9.3.0 , system |
C¶
c-ares - C3D - cadaver - CaDiCaL - CAFE5 - Caffe - cairo - cairomm - Calcam - Calendrical - Calib - CAMPARI - Cantera - canu - Canvas - CAP3 - CapnProto - captum - Cargo - Carma - carputils - Cartopy - casacore - Casanovo - CaSpER - CASPR - CASTEP - CastXML - CAT-BAT - Catch2 - category_encoders - CatLearn - CatMAP - causallift - causalml - CaVEMan - CAVIAR - Cbc - CBLAS - ccache - CCfits - CCL - cclib - cctools - CD-HIT - CDAT - cdbfasta - CDBtools - cddlib - CDFlib - cDNA_Cupcake - CDO - cdo-bindings - cdsapi - cell2location - CellChat - CellMix - CellOracle - Cellpose - CellRanger - CellRanger-ARC - CellRanger-ATAC - CellRank - CellTypist - Centrifuge - Cereal - CESM-deps - CFDEMcoupling - CFITSIO - cftime - CGAL - cget - Cgl - CGmapTools - CGNS - CharLS - CHASE - Check - CheckM - CheckM-Database - Cheetah - Chemaxon-Marvin - chemprop - CheMPS2 - CHERAB - chewBBACA - chi2comb - Chimera - ChimPipe - Chromaprint - cicero - CIF2Cell - cimfomfa - CIRCexplorer - CIRCexplorer2 - Circos - CIRI - CIRI-long - cisTEM - CITE-seq-Count - Clang - Clang-AOMP - Clang-Python-bindings - CLAPACK - CLEASE - CLHEP - CliMetLab - CLIP - CLISP - ClonalFrameML - CLooG - CloudCompare - Clp - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CMAverse - CmdStanR - cmocean - CMSeq - CNT-ILP - CNVkit - CNVnator - Co-phylog - COBRApy - CoCoALib - CodAn - code-server - CODEX2 - CodingQuarry - Cogent - Coin - CoinUtils - ColabFold - colossalai - Commet - CompareM - Compress-Raw-Zlib - COMSOL - Con3F - conan - CONCOCT - configparser - configurable-http-proxy - CONN - ConnectomeWorkbench - Control-FREEC - cooler - CoordgenLibs - Coot - CopyKAT - core-counter - Coreutils - corner - CoSymLib - coverage - cowsay - CP2K - CPB - CPC2 - CPLEX - CPPE - CppUnit - cppy - cppzmq - cpu_features - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CREST - CRF++ - CRISPR-DAV - CRISPResso2 - cromwell - crossguid - CrossMap - CrossTalkZ - CRPropa - Crumble - cryoCARE - cryoDRGN - CryptoMiniSat - CrystFEL - CSB - CSBDeep - CSBLAST - cscope - csvkit - ctags - ctffind - CTPL - Cube - CubeGUI - CubeLib - CubeWriter - CUDA - CUDA-Samples - CUDAcompat - CUDAcore - cuDNN - Cufflinks - CUnit - CuPy - cURL - cuSPARSELt - custodian - cutadapt - cuTENSOR - CVS - CVXOPT - CVXPY - CWIPI - cwltool - cxxopts - cysignals - Cython - cython-blis - cytoolz - Cytoscape - cytosim - cyvcf2
c-ares¶
c-ares is a C library for asynchronous DNS requests (including name resolves)
homepage: https://c-ares.org/
version | toolchain |
---|---|
1.17.2 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
1.18.1 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
C3D¶
Convert3D Medical Image Processing Tool
homepage: https://sourceforge.net/projects/c3d/
version | toolchain |
---|---|
1.0.0 |
system |
cadaver¶
cadaver is a command-line WebDAV client for Unix.
homepage: http://www.webdav.org/cadaver/
version | toolchain |
---|---|
0.23.3 |
intel/2017a |
CaDiCaL¶
CaDiCaL is a simplified satisfiability solver. The original goal of the development of CaDiCaL was to obtain a CDCL solver, which is easy to understand and change, while at the same time not being much slower than other state-of-the-art CDCL solvers.
homepage: https://github.com/arminbiere/cadical
version | toolchain |
---|---|
1.3.0 |
GCC/9.3.0 |
CAFE5¶
Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.
homepage: https://github.com/hahnlab/CAFE5
version | toolchain |
---|---|
5.0.0 |
GCC/10.2.0 |
Caffe¶
Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors.
homepage: https://github.com/BVLC/caffe
version | versionsuffix | toolchain |
---|---|---|
1.0 |
-CUDA-9.1.85-Python-2.7.14 |
intel/2017b |
1.0 |
-Python-2.7.13 |
intel/2017a |
1.0 |
-Python-2.7.14 |
intel/2017b |
rc3 |
-CUDA-7.5.18-Python-2.7.11 |
foss/2016a |
cairo¶
Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
homepage: https://cairographics.org
version | versionsuffix | toolchain |
---|---|---|
1.14.6 |
foss/2016a , foss/2016b , intel/2016a , intel/2016b |
|
1.14.6 |
-GLib-2.48.0 |
foss/2016a , intel/2016a |
1.14.8 |
intel/2017a |
|
1.14.10 |
GCCcore/6.3.0 , GCCcore/6.4.0 , intel/2017b |
|
1.14.12 |
GCCcore/6.4.0 , GCCcore/7.3.0 |
|
1.16.0 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
|
1.17.4 |
GCCcore/11.3.0 , GCCcore/12.2.0 |
cairomm¶
The Cairomm package provides a C++ interface to Cairo.
homepage: http://cairographics.org
version | toolchain |
---|---|
1.12.2 |
GCCcore/6.4.0 , GCCcore/7.3.0 |
Calcam¶
Calcam is a Python package providing tools for spatial calibration of cameras, i.e. determining the mapping between pixel coordinates in an image and real-world 3D sight lines & coordinates.
homepage: https://euratom-software.github.io/calcam
version | versionsuffix | toolchain |
---|---|---|
2.1.0 |
-Python-2.7.14 |
intel/2018a |
2.1.0 |
-Python-3.6.4 |
intel/2018a |
Calendrical¶
Calendrical module is for calendrical calculations.
homepage: https://www.funaba.org/code#calendrical
version | versionsuffix | toolchain |
---|---|---|
2.0.1 |
-Python-3.6.3 |
intel/2017b |
2.0.2a |
-Python-3.6.4 |
intel/2018a |
2.0.2a |
-Python-3.6.6 |
intel/2018b |
Calib¶
Calib clusters paired-end reads using their barcodes and sequences. Calib is suitable for amplicon sequencing where a molecule is tagged, then PCR amplified with high depth, also known as Unique Molecule Identifier (UMI) sequencing.
homepage: https://github.com/vpc-ccg/calib
version | toolchain |
---|---|
0.3.4 |
GCC/9.3.0 |
CAMPARI¶
CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion.
homepage: http://campari.sourceforge.net/V4/index.html
version | toolchain |
---|---|
4.0 |
intel/2020b |
Cantera¶
Chemical kinetics, thermodynamics, and transport tool suite
homepage: https://github.com/Cantera/cantera
version | versionsuffix | toolchain |
---|---|---|
2.2.1 |
-Python-2.7.12 |
intel/2016b |
2.3.0 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
2.3.0 |
-Python-2.7.13 |
intel/2017a |
2.3.0 |
-Python-2.7.14 |
foss/2017b , intel/2017b , intel/2018a |
2.4.0 |
-Python-2.7.14 |
intel/2018a |
2.6.0 |
foss/2022a |
canu¶
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing
homepage: https://canu.readthedocs.io
version | versionsuffix | toolchain |
---|---|---|
1.4 |
foss/2016b |
|
1.7 |
intel/2018a |
|
1.8 |
-Perl-5.26.0 |
foss/2017b , intel/2017b |
1.8 |
-Perl-5.28.0 |
foss/2018b |
1.8 |
-Perl-5.28.1 |
GCCcore/8.2.0 |
1.9 |
-Java-11 |
GCCcore/8.3.0 |
2.1.1 |
GCCcore/10.2.0 |
|
2.1.1 |
-Java-11 |
GCCcore/9.3.0 |
2.2 |
GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 |
|
2.2 |
-Java-11 |
GCCcore/10.3.0 |
Canvas¶
Copy number variant (CNV) calling from DNA sequencing data
homepage: https://github.com/Illumina/canvas
version | toolchain |
---|---|
1.39.0.1598 |
system |
CAP3¶
CAP3 assembly program
homepage: http://seq.cs.iastate.edu/
version | toolchain |
---|---|
20071221-intel-x86 |
system |
20071221-intel-x86_64 |
system |
20071221-opteron |
system |
CapnProto¶
Cap’n Proto is an insanely fast data interchange format and capability-based RPC system.
homepage: https://capnproto.org
version | toolchain |
---|---|
0.6.1 |
GCCcore/6.4.0 |
0.7.0 |
GCCcore/7.3.0 |
0.8.0 |
GCCcore/9.3.0 |
0.9.1 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 |
0.10.2 |
GCCcore/11.3.0 |
0.10.3 |
GCCcore/12.2.0 |
captum¶
Captum is a model interpretability and understanding library for PyTorch. Captum means comprehension in Latin and contains general purpose implementations of integrated gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. It has quick integration for models built with domain-specific libraries such as torchvision, torchtext, and others.
homepage: https://captum.ai/
version | versionsuffix | toolchain |
---|---|---|
0.5.0 |
foss/2022a |
|
0.5.0 |
-CUDA-11.7.0 |
foss/2022a |
Cargo¶
The Rust package manager
homepage: https://crates.io/
version | toolchain |
---|---|
0.13.0 |
foss/2016b |
Carma¶
Carma - A molecular dynamics analysis program
homepage: http://utopia.duth.gr/~glykos/Carma.html
version | toolchain |
---|---|
2.01 |
foss/2019b |
carputils¶
carputils is a Python framework for generating and running openCARP examples.
homepage: https://git.opencarp.org/openCARP/carputils
version | versionsuffix | toolchain |
---|---|---|
20200915 |
-Python-3.8.2 |
foss/2020a |
20210513 |
foss/2020b |
Cartopy¶
Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.
homepage: https://scitools.org.uk/cartopy/docs/latest/
version | versionsuffix | toolchain |
---|---|---|
0.18.0 |
-Python-3.7.4 |
foss/2019b |
0.18.0 |
-Python-3.8.2 |
foss/2020a |
0.19.0.post1 |
foss/2020b , intel/2020b |
|
0.20.0 |
foss/2021a |
|
0.20.3 |
foss/2021b , foss/2022a |
casacore¶
A suite of C++ libraries for radio astronomy data processing. The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. Thus user's can update them.
homepage: https://github.com/casacore/casacore
version | toolchain |
---|---|
3.4.0 |
foss/2021b |
Casanovo¶
De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
homepage: https://casanovo.readthedocs.io
version | versionsuffix | toolchain |
---|---|---|
3.3.0 |
foss/2022a |
|
3.3.0 |
-CUDA-11.7.0 |
foss/2022a |
CaSpER¶
CaSpER is a signal processing approach for identification, visualization, and integrative analysis of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data.
homepage: https://github.com/akdess/CaSpER
version | toolchain |
---|---|
2.0 |
foss/2019b |
CASPR¶
Running CASPR is extremely easy and convenient to analyze CRIPR-Cas9 screens using pgRNAs.
homepage: https://judithbergada.github.io/CASPR
version | toolchain |
---|---|
20200730 |
foss/2022a |
CASTEP¶
CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.
homepage: http://www.castep.org
version | toolchain |
---|---|
21.1.1 |
CrayCCE/19.06 , CrayGNU/19.06 , foss/2019b , intel/2019b , iomkl/2019b |
22.11 |
foss/2022a |
CastXML¶
CastXML is a C-family abstract syntax tree XML output tool.
homepage: https://github.com/CastXML/CastXML
version | toolchain |
---|---|
0.4.3 |
GCCcore/8.3.0 |
20160617 |
foss/2016a |
20180806 |
foss/2018a |
CAT-BAT¶
Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs).
homepage: https://github.com/dutilh/CAT
version | toolchain |
---|---|
5.2.3 |
GCC/10.3.0 |
Catch2¶
A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch)
homepage: https://github.com/catchorg/Catch2
version | toolchain |
---|---|
2.9.1 |
system |
2.11.0 |
system |
2.13.4 |
system |
category_encoders¶
A set of scikit-learn-style transformers for encoding categorical variables into numeric by means of different techniques.
homepage: https://github.com/scikit-learn-contrib/category_encoders
version | toolchain |
---|---|
2.4.1 |
foss/2021b |
CatLearn¶
An environment for atomistic machine learning in Python for applications in catalysis
homepage: https://catlearn.readthedocs.io
version | toolchain |
---|---|
0.6.2 |
intel/2022a |
CatMAP¶
Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening.
homepage: https://catmap.readthedocs.io
version | versionsuffix | toolchain |
---|---|---|
20170927 |
-Python-2.7.14 |
intel/2017b |
20220519 |
foss/2022a |
causallift¶
CausalLift: Python package for Uplift Modeling in real-world business; applicable for both A/B testing and observational data
homepage: https://github.com/Minyus/causallift
version | versionsuffix | toolchain |
---|---|---|
1.0.6 |
-Python-3.8.2 |
foss/2020a |
causalml¶
Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML
homepage: https://github.com/uber/causalml
version | versionsuffix | toolchain |
---|---|---|
0.3.0-20180610 |
-Python-3.7.2 |
foss/2019a |
0.8.0-20200909 |
-Python-3.8.2 |
foss/2020a |
CaVEMan¶
SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
homepage: http://cancerit.github.io/CaVEMan/
version | toolchain |
---|---|
1.13.2 |
foss/2018a |
CAVIAR¶
CAusal Variants Identication in Associated Regions. A statistical framework that quantifies the probability of each variant to be causal while allowing an arbitrary number of causal variants.
homepage: https://github.com/fhormoz/caviar
version | toolchain |
---|---|
2.2-20190419 |
foss/2019b |
Cbc¶
Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.
homepage: https://github.com/coin-or/Cbc
version | toolchain |
---|---|
2.10.3 |
foss/2018b |
2.10.5 |
foss/2020b , foss/2021a |
CBLAS¶
C interface to the BLAS
homepage: https://www.netlib.org/blas/
version | toolchain |
---|---|
20110120 |
foss/2016b , intel/2019b , intel/2020a |
ccache¶
Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again
homepage: https://ccache.dev/
version | versionsuffix | toolchain |
---|---|---|
3.2.5 |
system |
|
3.3.1 |
system |
|
3.3.3 |
system |
|
3.3.4 |
-f90 |
system |
3.7.11 |
system |
|
4.2.1 |
system |
|
4.6.1 |
GCCcore/11.2.0 |
|
4.6.3 |
system |
CCfits¶
CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++.
homepage: https://heasarc.gsfc.nasa.gov/fitsio/CCfits/
version | toolchain |
---|---|
2.5 |
GCCcore/9.3.0 |
CCL¶
Clozure CL (often called CCL for short) is a free Common Lisp implementation with a long history. Some distinguishing features of the implementation include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface.
homepage: https://ccl.clozure.com/
version | toolchain |
---|---|
1.11.5 |
system |
1.12 |
GCCcore/9.3.0 |
1.12.1 |
GCCcore/10.3.0 |
cclib¶
cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner.
homepage: https://cclib.github.io/
version | versionsuffix | toolchain |
---|---|---|
1.5 |
-Python-3.5.2 |
foss/2016b |
1.6.3 |
-Python-3.8.2 |
foss/2020a , intel/2020a |
1.7.2 |
foss/2021b |
cctools¶
The Cooperating Computing Tools (CCTools) help you to design and deploy scalable applications that run on hundreds or thousands of machines at once.
homepage: https://ccl.cse.nd.edu/
version | toolchain |
---|---|
7.0.22 |
GCCcore/8.3.0 |
CD-HIT¶
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
homepage: https://github.com/weizhongli/cdhit
version | versionsuffix | toolchain |
---|---|---|
4.6.4 |
-2015-0603 |
GNU/4.9.3-2.25 |
4.6.6 |
foss/2016b |
|
4.6.8 |
foss/2018b , intel/2017a , intel/2018a |
|
4.8.1 |
GCC/10.2.0 , GCC/10.3.0 , GCC/11.2.0 , GCC/11.3.0 , GCC/8.3.0 , GCC/9.3.0 , foss/2018b , iccifort/2019.5.281 |
CDAT¶
CDAT is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for data analysis problems.
homepage: https://github.com/CDAT/cdat
version | versionsuffix | toolchain |
---|---|---|
8.2.1 |
-Python-3.8.2 |
foss/2020a |
cdbfasta¶
Fasta file indexing and retrival tool
homepage: https://sourceforge.net/projects/cdbfasta
version | toolchain |
---|---|
0.99 |
GCC/8.3.0 , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , iccifort/2019.5.281 |
CDBtools¶
CDB (Constant DataBase) indexing and retrieval tools for FASTA files
homepage: http://compbio.dfci.harvard.edu/tgi
version | toolchain |
---|---|
0.99 |
GCC/10.2.0 , GCC/11.3.0 |
cddlib¶
An efficient implementation of the Double Description Method
homepage: https://github.com/cddlib/cddlib
version | toolchain |
---|---|
0.94i |
GCCcore/8.2.0 |
0.94j |
GCCcore/8.3.0 |
CDFlib¶
cdflib is a python module to read/write CDF (Common Data Format .cdf) files without needing to install the CDF NASA library.
homepage: https://github.com/MAVENSDC/cdflib
version | toolchain |
---|---|
0.4.9 |
foss/2022a |
cDNA_Cupcake¶
cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
homepage: https://github.com/Magdoll/cDNA_Cupcake
version | versionsuffix | toolchain |
---|---|---|
5.8 |
-Python-2.7.14 |
intel/2018a |
24.2.0 |
-Python-3.8.2 |
foss/2020a |
26.0.0 |
foss/2021a |
CDO¶
CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
homepage: https://code.zmaw.de/projects/cdo
version | toolchain |
---|---|
1.7.2 |
intel/2016b |
1.8.1 |
intel/2017a |
1.9.1 |
intel/2017b |
1.9.2 |
intel/2017b |
1.9.5 |
intel/2018a , intel/2018b , iomkl/2018b |
1.9.8 |
intel/2019b |
1.9.10 |
gompi/2019b , gompi/2020b , gompi/2021a , iimpi/2021b |
2.0.5 |
gompi/2021b |
2.0.6 |
gompi/2022a |
2.1.1 |
gompi/2021a |
cdo-bindings¶
Python interface to CDO.
homepage: https://github.com/Try2Code/cdo-bindings
version | toolchain |
---|---|
1.5.7 |
foss/2021b |
cdsapi¶
Climate Data Store API
homepage: https://pypi.org/project/cdsapi
version | versionsuffix | toolchain |
---|---|---|
0.1.4 |
foss/2019a |
|
0.1.4 |
-Python-3.6.6 |
foss/2018b |
0.3.0 |
GCCcore/9.3.0 |
|
0.5.1 |
GCCcore/11.3.0 |
cell2location¶
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
homepage: https://github.com/BayraktarLab/cell2location/
version | toolchain |
---|---|
0.05-alpha |
fosscuda/2020b |
CellChat¶
" R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
homepage: https://github.com/sqjin/CellChat
version | toolchain |
---|---|
1.5.0 |
foss/2022a |
CellMix¶
A Comprehensive Toolbox for Gene Expression Deconvolution
homepage: http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix
version | versionsuffix | toolchain |
---|---|---|
1.6.2 |
-R-3.5.1 |
foss/2018b |
CellOracle¶
CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data and Gene Regulatory Network models.
homepage: https://github.com/morris-lab/CellOracle
version | toolchain |
---|---|
0.12.0 |
foss/2022a |
Cellpose¶
a generalist algorithm for cellular segmentation
homepage: https://www.cellpose.org/
version | toolchain |
---|---|
0.6.5 |
foss/2020b , fosscuda/2020b |
CellRanger¶
Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
version | toolchain |
---|---|
3.0.0 |
system |
3.0.2 |
system |
3.1.0 |
system |
4.0.0 |
system |
5.0.0 |
system |
5.0.1 |
system |
6.0.0 |
system |
6.0.1 |
system |
6.0.2 |
system |
6.1.2 |
system |
7.0.0 |
system |
7.1.0 |
system |
CellRanger-ARC¶
Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression.
version | toolchain |
---|---|
1.0.1 |
system |
2.0.0 |
system |
2.0.1 |
system |
CellRanger-ATAC¶
Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
version | toolchain |
---|---|
1.2.0 |
system |
2.0.0 |
system |
2.1.0 |
system |
CellRank¶
CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. It contains two main modules: kernels compute cell-cell transition probabilities and estimators generate hypothesis based on these.
homepage: https://cellrank.readthedocs.io/en/stable/
version | toolchain |
---|---|
1.4.0 |
foss/2021a |
CellTypist¶
A tool for semi-automatic cell type annotation
homepage: https://www.celltypist.org/
version | toolchain |
---|---|
1.0.0 |
foss/2021b |
Centrifuge¶
Classifier for metagenomic sequences
homepage: https://ccb.jhu.edu/software/centrifuge
version | toolchain |
---|---|
1.0.3 |
foss/2018b |
1.0.4 |
gompi/2020b , gompi/2021a |
1.0.4-beta |
foss/2018b , gompi/2020a |
Cereal¶
cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
homepage: https://uscilab.github.io/cereal/
version | toolchain |
---|---|
1.3.0 |
system |
1.3.2 |
system |
CESM-deps¶
CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
homepage: https://www.cesm.ucar.edu/models/cesm2/
version | toolchain |
---|---|
2 |
foss/2018b , foss/2021b , intel/2018b , iomkl/2018b |
CFDEMcoupling¶
CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple the DEM engine LIGGGHTS to a CFD framework.
homepage: https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework
version | toolchain |
---|---|
3.8.0 |
foss/2018a |
CFITSIO¶
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
homepage: https://heasarc.gsfc.nasa.gov/fitsio/
version | toolchain |
---|---|
3.38 |
foss/2016a , intel/2016a |
3.41 |
GCCcore/5.4.0 , GCCcore/6.3.0 , intel/2016b |
3.42 |
GCCcore/6.4.0 , intel/2017b |
3.45 |
GCCcore/7.3.0 , intel/2018b |
3.47 |
GCCcore/8.2.0 , GCCcore/8.3.0 |
3.48 |
GCCcore/9.3.0 |
3.49 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 |
4.2.0 |
GCCcore/11.3.0 , GCCcore/12.2.0 |
cftime¶
Time-handling functionality from netcdf4-python
homepage: https://github.com/Unidata/cftime
version | versionsuffix | toolchain |
---|---|---|
1.0.0 |
-Python-3.6.4 |
intel/2018a |
1.0.0b1 |
-Python-3.6.2 |
foss/2017b |
1.0.1 |
-Python-2.7.15 |
intel/2018b |
1.0.1 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
CGAL¶
The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
homepage: https://www.cgal.org/
version | versionsuffix | toolchain |
---|---|---|
4.8 |
-Python-2.7.11 |
foss/2016a , intel/2016a |
4.8.1 |
foss/2016b , intel/2016b |
|
4.8.1 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
4.9 |
-Python-2.7.12 |
intel/2016b |
4.9 |
-Python-2.7.13 |
intel/2017a |
4.11 |
-Python-2.7.13 |
intel/2017a |
4.11 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
4.11 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
4.11.1 |
-Python-2.7.14 |
foss/2018a , intel/2018a |
4.11.1 |
-Python-2.7.15 |
foss/2018b |
4.11.1 |
-Python-3.6.4 |
foss/2018a |
4.11.1 |
-Python-3.6.6 |
foss/2018b |
4.14 |
-Python-3.7.2 |
foss/2019a , intel/2019a |
4.14.1 |
-Python-3.7.4 |
foss/2019b , intel/2019b |
4.14.3 |
gompi/2021a , gompi/2021b , gompi/2022a , iimpi/2021a |
|
4.14.3 |
-Python-3.8.2 |
gompi/2020a , iimpi/2020a |
5.2 |
gompi/2020b |
cget¶
Cmake package retrieval. This can be used to download and install cmake packages
homepage: https://cget.readthedocs.io/en/latest/index.html
version | versionsuffix | toolchain |
---|---|---|
0.1.6 |
-Python-3.6.4 |
foss/2018a |
Cgl¶
The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.
homepage: https://github.com/coin-or/Cgl
version | toolchain |
---|---|
0.60.2 |
foss/2018b |
0.60.3 |
foss/2020b , foss/2021a |
CGmapTools¶
Command-line Toolset for Bisulfite Sequencing Data Analysis
homepage: https://cgmaptools.github.io/
version | toolchain |
---|---|
0.1.2 |
intel/2019b |
CGNS¶
The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data.
homepage: https://cgns.github.io/
version | toolchain |
---|---|
3.3.1 |
foss/2016b |
4.1.0 |
intelcuda/2019b |
CharLS¶
CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios.
homepage: https://github.com/team-charls/charls
version | toolchain |
---|---|
2.0.0 |
GCCcore/6.4.0 , GCCcore/7.3.0 |
2.1.0 |
GCCcore/8.2.0 , GCCcore/8.3.0 |
2.2.0 |
GCCcore/10.2.0 |
2.3.4 |
GCCcore/10.3.0 |
2.4.1 |
GCCcore/11.3.0 |
CHASE¶
Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies.
homepage: http://people.duke.edu/~asallen/Software.html
version | toolchain |
---|---|
20130626 |
system |
Check¶
Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.
homepage: https://libcheck.github.io/check/
version | toolchain |
---|---|
0.12.0 |
GCCcore/6.4.0 |
0.15.2 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/9.3.0 |
CheckM¶
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
homepage: https://github.com/Ecogenomics/CheckM
version | versionsuffix | toolchain |
---|---|---|
1.0.13 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
1.0.13 |
-Python-2.7.15 |
foss/2018b |
1.0.13 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
1.0.18 |
-Python-2.7.15 |
foss/2019a |
1.0.18 |
-Python-2.7.18 |
foss/2020b |
1.1.2 |
-Python-3.7.4 |
foss/2019b , intel/2019b |
1.1.3 |
foss/2021a , foss/2021b |
|
1.1.3 |
-Python-3.8.2 |
intel/2020a |
1.2.2 |
foss/2022a |
CheckM-Database¶
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. This is the corresponding database.
homepage: https://github.com/Ecogenomics/CheckM
version | toolchain |
---|---|
2015_01_16 |
system |
Cheetah¶
Cheetah is an open source template engine and code generation tool.
homepage: https://cheetahtemplate.org
version | versionsuffix | toolchain |
---|---|---|
2.4.4 |
-Python-2.7.15 |
intel/2018b |
Chemaxon-Marvin¶
Marvin suite is a chemically intelligent desktop toolkit built to help you draw, edit, publish, render, import and export your chemical structures and as well as allowing you to convert between various chemical and graphical file formats. It is free for individual, academic and non-commercial use.
homepage: https://chemaxon.com/products/marvin
version | toolchain |
---|---|
21.14 |
system |
chemprop¶
Message Passing Neural Networks for Molecule Property Prediction
homepage: https://github.com/chemprop/chemprop
version | versionsuffix | toolchain |
---|---|---|
1.5.2 |
foss/2022a |
|
1.5.2 |
-CUDA-11.7.0 |
foss/2022a |
CheMPS2¶
CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
homepage: https://github.com/SebWouters/CheMPS2
version | toolchain |
---|---|
1.6 |
intel/2016a |
1.7-rc2 |
intel/2016a |
1.7.1 |
intel/2016a |
1.7.2 |
intel/2016a |
1.8 |
intel/2016b |
1.8.8 |
intel/2018b |
1.8.9 |
foss/2018b , foss/2019a , intel/2018b , intel/2019a , intel/2019b |
1.8.11 |
foss/2021b |
1.8.12 |
foss/2022a |
CHERAB¶
CHERAB is a python library for forward modelling diagnostics based on spectroscopic plasma emission.
homepage: https://cherab.github.io/documentation/index.html
version | versionsuffix | toolchain |
---|---|---|
1.2.0 |
-Python-3.6.6 |
intel/2018b |
1.3.0 |
foss/2020b , intel/2020b |
chewBBACA¶
chewBBACA stands for "BSR-Based Allele Calling Algorithm". chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.
homepage: https://github.com/B-UMMI/chewBBACA
version | versionsuffix | toolchain |
---|---|---|
2.5.5 |
-Python-3.8.2 |
intel/2020a |
chi2comb¶
Cumulative density function of linear combinations of independent chi-square random variables and a standard Normal distribution. As of now, this is basically a repackaging of the davies function implemented in the CompQuadForm library for R.
homepage: https://github.com/limix/chi2comb
version | toolchain |
---|---|
0.0.3 |
GCCcore/7.3.0 |
Chimera¶
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
homepage: https://www.cgl.ucsf.edu/chimera/
version | versionsuffix | toolchain |
---|---|---|
1.10 |
-linux_x86_64 |
system |
1.16 |
-linux_x86_64 |
system |
ChimPipe¶
ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution.
homepage: https://chimpipe.readthedocs.org/
version | versionsuffix | toolchain |
---|---|---|
0.9.5 |
foss/2018b |
|
0.9.5 |
-Python-2.7.12 |
foss/2016b |
Chromaprint¶
Chromaprint is the core component of the AcoustID project. It's a client-side library that implements a custom algorithm for extracting fingerprints from any audio source.
homepage: https://acoustid.org/chromaprint
version | toolchain |
---|---|
1.4.3 |
GCCcore/8.2.0 |
cicero¶
Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments.
homepage: https://cole-trapnell-lab.github.io/cicero-release
version | versionsuffix | toolchain |
---|---|---|
1.3.4.11 |
-R-4.0.3-Monocle3 |
foss/2020b |
CIF2Cell¶
CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files.
homepage: https://sourceforge.net/projects/cif2cell
version | versionsuffix | toolchain |
---|---|---|
1.2.10 |
-Python-2.7.16 |
GCCcore/8.3.0 |
cimfomfa¶
This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. Both understandably and regrettably I chose long ago to make it C-string-compatible, hence nul bytes may not be part of a string. At some point I hope to rectify this, perhaps unrealistically.
homepage: https://github.com/micans/cimfomfa
version | toolchain |
---|---|
22.273 |
GCCcore/11.3.0 |
CIRCexplorer¶
CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.
homepage: https://circexplorer2.readthedocs.io/
version | versionsuffix | toolchain |
---|---|---|
1.1.10 |
-Python-2.7.14 |
intel/2017b |
CIRCexplorer2¶
CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset.
homepage: http://circexplorer2.readthedocs.io/
version | versionsuffix | toolchain |
---|---|---|
2.3.2 |
-Python-2.7.14 |
intel/2017b |
2.3.3 |
-Python-2.7.14 |
intel/2018a |
2.3.8 |
-Python-2.7.18 |
foss/2020b |
Circos¶
Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
homepage: http://www.circos.ca/
version | versionsuffix | toolchain |
---|---|---|
0.69-5 |
-Perl-5.24.0 |
foss/2016b |
0.69-6 |
-Perl-5.26.1 |
GCCcore/6.4.0 |
0.69-6 |
-Perl-5.28.0 |
GCCcore/7.3.0 |
0.69-9 |
GCCcore/11.3.0 , GCCcore/9.3.0 |
CIRI¶
CircRNA Identifier. A de novo circular RNA identification tool
homepage: https://sourceforge.net/projects/ciri/
version | versionsuffix | toolchain |
---|---|---|
2.0.6 |
-Perl-5.26.0 |
intel/2017b |
CIRI-long¶
Circular RNA Identification for Long-Reads Nanopore Sequencing Data
homepage: https://github.com/bioinfo-biols/CIRI-long/
version | toolchain |
---|---|
1.0.2 |
foss/2020b |
cisTEM¶
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
homepage: https://cistem.org/
version | toolchain |
---|---|
1.0.0-beta |
foss/2018a |
CITE-seq-Count¶
A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.
homepage: https://github.com/Hoohm/CITE-seq-Count
version | versionsuffix | toolchain |
---|---|---|
1.4.3 |
-Python-3.6.6 |
foss/2018b |
1.4.3 |
-Python-3.7.4 |
foss/2019b |
Clang¶
C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
homepage: https://clang.llvm.org/
version | versionsuffix | toolchain |
---|---|---|
3.3 |
GCC/4.8.1 |
|
3.4 |
GCC/4.8.2 |
|
3.4.1 |
GCC/4.8.2 |
|
3.4.2 |
GCC/4.8.2 |
|
3.6.0 |
GCC/4.9.2 |
|
3.6.1 |
GCC/4.9.2 |
|
3.7.0 |
GNU/4.9.3-2.25 |
|
3.7.1 |
GCC/4.9.3-2.25 , foss/2016a |
|
3.8.0 |
GCC/4.9.3-2.25 |
|
3.8.1 |
GCC/5.4.0-2.26 , foss/2016b |
|
5.0.0 |
GCC/6.4.0-2.28 |
|
5.0.1 |
GCC/6.4.0-2.28 |
|
6.0.1 |
GCC/6.4.0-2.28 , GCC/7.3.0-2.30 |
|
7.0.0 |
GCC/6.4.0-2.28 |
|
7.0.1 |
GCC/7.3.0-2.30 |
|
8.0.0 |
GCCcore/8.2.0 |
|
8.0.0 |
-CUDA-10.1.105 |
GCCcore/8.2.0 |
8.0.1 |
-CUDA-10.1.105 |
GCC/8.2.0-2.31.1 |
8.0.1 |
-CUDA-10.1.243 |
GCC/8.3.0 |
9.0.1 |
GCCcore/8.3.0 , GCCcore/9.3.0 |
|
9.0.1 |
-CUDA-10.1.243 |
GCC/8.3.0 |
10.0.0 |
GCCcore/8.3.0 , GCCcore/9.3.0 |
|
10.0.1 |
GCCcore/9.3.0 |
|
11.0.0 |
GCCcore/9.3.0 |
|
11.0.1 |
GCCcore/10.2.0 , gcccuda/2020b |
|
12.0.1 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
|
12.0.1 |
-CUDA-11.3.1 |
GCCcore/10.3.0 |
13.0.1 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
|
13.0.1 |
-CUDA-11.4.1 |
GCCcore/11.2.0 |
15.0.5 |
GCCcore/11.3.0 |
Clang-AOMP¶
AOMP is an open source Clang/LLVM based compiler with added support for the OpenMP® API on Radeon™ GPUs.
homepage: https://github.com/RadeonOpenCompute/llvm-project
version | toolchain |
---|---|
4.5.0 |
GCCcore/11.2.0 |
Clang-Python-bindings¶
Python bindings for libclang
homepage: https://clang.llvm.org
version | versionsuffix | toolchain |
---|---|---|
8.0.0 |
-Python-2.7.15 |
GCCcore/8.2.0 |
10.0.1 |
-Python-3.8.2 |
GCCcore/9.3.0 |
13.0.1 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
CLAPACK¶
C version of LAPACK
homepage: http://www.netlib.org/clapack
version | toolchain |
---|---|
3.2.1 |
GCC/6.4.0-2.28 , iccifort/2017.4.196-GCC-6.4.0-2.28 , intel/2017a |
CLEASE¶
CLuster Expansion in Atomic Simulation Environment (CLEASE) is a package that automates the cumbersome setup and construction procedure of cluster expansion (CE). It provides a comprehensive list of tools for specifying parameters for CE, generating training structures, fitting effective cluster interaction (ECI) values and running Monte Carlo simulations.
homepage: https://gitlab.com/computationalmaterials/clease
version | toolchain |
---|---|
0.10.6 |
intel/2021a |
CLHEP¶
The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.
homepage: https://proj-clhep.web.cern.ch/proj-clhep/
version | toolchain |
---|---|
2.1.1.0 |
intel/2016a |
2.1.3.1 |
intel/2016a |
2.2.0.8 |
intel/2016a |
2.3.1.1 |
intel/2016a |
2.3.4.3 |
foss/2017b , intel/2017b |
2.4.0.0 |
intel/2017b |
2.4.1.0 |
foss/2017b , foss/2018b , intel/2017b , intel/2018b |
2.4.1.3 |
foss/2019b , foss/2020a |
2.4.4.0 |
GCC/10.2.0 , GCC/11.2.0 |
2.4.5.1 |
GCC/11.2.0 |
2.4.6.4 |
GCC/12.2.0 |
CliMetLab¶
CliMetLab is a Python package aiming at simplifying access to climate and meteorological datasets, allowing users to focus on science instead of technical issues such as data access and data formats. It is mostly intended to be used in Jupyter notebooks, and be interoperable with all popular data analytic packages, such as Numpy, Pandas, Xarray, SciPy, Matplotlib, etc. as well as machine learning frameworks, such as Tensorflow, Keras or PyTorch.
homepage: https://climetlab.readthedocs.io/
version | toolchain |
---|---|
0.12.6 |
foss/2022a |
CLIP¶
CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a variety of (image, text) pairs. It can be instructed in natural language to predict the most relevant text snippet, given an image, without directly optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and 3.
homepage: https://github.com/openai/CLIP
version | versionsuffix | toolchain |
---|---|---|
20230220 |
-CUDA-11.7.0 |
foss/2022a |
CLISP¶
Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language.
homepage: https://clisp.sourceforge.io/
version | toolchain |
---|---|
2.49 |
GCCcore/6.4.0 , GCCcore/9.3.0 |
ClonalFrameML¶
Efficient Inference of Recombination in Whole Bacterial Genomes
homepage: https://github.com/xavierdidelot/ClonalFrameML
version | toolchain |
---|---|
1.11 |
foss/2016b |
CLooG¶
CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code.
homepage: http://www.bastoul.net/cloog/index.php
version | toolchain |
---|---|
0.18.1 |
GCC/4.8.2 |
CloudCompare¶
3D point cloud and mesh processing software
homepage: https://www.cloudcompare.org/
version | toolchain |
---|---|
2.12.4 |
foss/2021b |
Clp¶
Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available.
homepage: https://github.com/coin-or/Clp
version | toolchain |
---|---|
1.17.3 |
foss/2018b |
1.17.6 |
foss/2020b , foss/2021a |
1.17.7 |
foss/2021b |
Clustal-Omega¶
Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
homepage: http://www.clustal.org/omega/
version | toolchain |
---|---|
1.2.0 |
foss/2016b |
1.2.4 |
GCC/10.2.0 , GCC/10.3.0 , GCC/8.3.0 , foss/2018b , intel-compilers/2021.2.0 , intel/2018a , intel/2018b |
ClustalW2¶
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
homepage: https://www.ebi.ac.uk/Tools/msa/clustalw2/
version | toolchain |
---|---|
2.1 |
GCC/10.3.0 , GCC/11.2.0 , foss/2016b , foss/2018b , foss/2021a , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , intel/2017b , intel/2018b , intel/2020a |
Cluster-Buster¶
Cluster-Buster: Finding dense clusters of motifs in DNA sequences
homepage: https://github.com/weng-lab/cluster-buster/
version | toolchain |
---|---|
20160106 |
intel/2016a |
ClusterShell¶
ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters.
homepage: https://cea-hpc.github.io/clustershell/
version | toolchain |
---|---|
1.7.3 |
system |
CMake¶
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
homepage: https://www.cmake.org
version | toolchain |
---|---|
2.8.11 |
GCC/4.8.1 |
2.8.12 |
GCC/4.8.1 , GCC/4.8.2 |
3.0.0 |
GCC/4.8.3 |
3.1.0 |
GCC/4.9.2 |
3.1.3 |
GCC/4.9.2 , system |
3.2.1 |
GCC/4.9.2 , GNU/4.9.3-2.25 |
3.3.1 |
system |
3.3.2 |
GNU/4.9.3-2.25 , gimkl/2.11.5 |
3.4.1 |
GCC/4.9.2 , GCCcore/4.9.3 , foss/2016a , intel/2016.02-GCC-4.9 , intel/2016a , iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 |
3.4.3 |
foss/2016a , foss/2016b , gimkl/2.11.5 , intel/2016a |
3.5.1 |
intel/2016a |
3.5.2 |
GCC/4.9.3-2.25 , foss/2016a , foss/2016b , intel/2016a , intel/2016b , system |
3.6.1 |
GCC/5.4.0-2.26 , GCCcore/4.9.3 , foss/2016b , intel/2016b , system |
3.6.2 |
GCCcore/5.4.0 , foss/2016b , intel/2016b |
3.7.1 |
GCCcore/5.4.0 , GCCcore/6.2.0 , foss/2016b , intel/2016b |
3.7.2 |
GCCcore/6.3.0 , foss/2016b , intel/2016b |
3.8.0 |
GCCcore/6.3.0 |
3.8.1 |
GCCcore/6.3.0 |
3.8.2 |
GCCcore/6.3.0 |
3.9.1 |
GCCcore/6.3.0 , GCCcore/6.4.0 , system |
3.9.4 |
GCCcore/6.4.0 |
3.9.5 |
GCCcore/6.4.0 |
3.9.6 |
system |
3.10.0 |
GCCcore/6.4.0 |
3.10.1 |
GCCcore/6.4.0 |
3.10.2 |
GCCcore/6.4.0 , GCCcore/7.2.0 |
3.10.3 |
GCCcore/6.4.0 , GCCcore/7.2.0 |
3.11.1 |
GCCcore/6.4.0 |
3.11.4 |
GCCcore/6.4.0 , GCCcore/7.3.0 |
3.12.1 |
GCCcore/6.4.0 , GCCcore/7.2.0 , GCCcore/7.3.0 , system |
3.13.3 |
GCCcore/8.2.0 |
3.15.1 |
system |
3.15.3 |
GCCcore/8.3.0 |
3.16.4 |
GCCcore/9.3.0 |
3.18.4 |
GCCcore/10.2.0 , system |
3.20.1 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
3.21.1 |
GCCcore/11.2.0 |
3.22.1 |
GCCcore/11.2.0 |
3.23.1 |
GCCcore/11.3.0 |
3.24.3 |
GCCcore/11.3.0 , GCCcore/12.2.0 |
3.26.3 |
GCCcore/12.3.0 , GCCcore/13.1.0 |
CMAverse¶
The R package CMAverse provides a suite of functions for reproducible causal mediation analysis including cmdag for DAG visualization, cmest for statistical modeling and cmsens for sensitivity analysis.
homepage: https://bs1125.github.io/CMAverse/
version | toolchain |
---|---|
20220112 |
foss/2021b |
CmdStanR¶
CmdStanR is a lightweight interface to Stan for R users
homepage: https://mc-stan.org/cmdstanr
version | versionsuffix | toolchain |
---|---|---|
0.5.0 |
-R-4.1.2 |
foss/2021b |
cmocean¶
This package contains colormaps for commonly-used oceanographic variables. Most of the colormaps started from matplotlib colormaps, but have now been adjusted using the viscm tool to be perceptually uniform.
homepage: https://github.com/matplotlib/cmocean
version | toolchain |
---|---|
2.0 |
foss/2022a |
CMSeq¶
CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus.
homepage: https://github.com/SegataLab/cmseq/
version | versionsuffix | toolchain |
---|---|---|
1.0.3 |
-Python-3.8.2 |
foss/2020a |
1.0.4 |
foss/2022a |
CNT-ILP¶
Integer Linear Program for the Copy-Number Tree Problem
homepage: https://compbio.cs.brown.edu/projects/cnt-ilp/
version | toolchain |
---|---|
20171031 |
GCC/8.2.0-2.31.1 |
CNVkit¶
A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
homepage: https://github.com/etal/cnvkit
version | versionsuffix | toolchain |
---|---|---|
0.9.2 |
-Python-2.7.14 |
intel/2017b |
0.9.3 |
-Python-3.6.4 |
intel/2018a |
0.9.6 |
-Python-3.7.2-R-3.6.0 |
foss/2019a |
0.9.8 |
-R-4.0.3 |
foss/2020b |
CNVnator¶
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
homepage: https://github.com/abyzovlab/CNVnator
version | toolchain |
---|---|
0.3.3 |
foss/2016b |
Co-phylog¶
Co-phylog: an assembly-free phylogenomic approach for closely related organisms H Yi, L Jin Nucleic acids research 41 (7), e75-e75
homepage: https://github.com/yhg926/co-phylog
version | toolchain |
---|---|
20201012 |
GCC/7.3.0-2.30 |
COBRApy¶
COBRApy is a package for constraint-based modeling of metabolic networks.
homepage: https://opencobra.github.io/cobrapy/
version | toolchain |
---|---|
0.26.0 |
foss/2021a |
CoCoALib¶
CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra.
homepage: http://cocoa.dima.unige.it/cocoalib
version | toolchain |
---|---|
0.99601 |
GCC/8.2.0-2.31.1 |
0.99700 |
GCC/8.3.0 |
CodAn¶
CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species.
homepage: https://github.com/pedronachtigall/CodAn
version | toolchain |
---|---|
1.2 |
foss/2021b |
code-server¶
Run VS Code on any machine anywhere and access it in the browser.
homepage: https://github.com/cdr/code-server
version | toolchain |
---|---|
3.7.3 |
system |
4.9.1 |
system |
CODEX2¶
Full-spectrum copy number variation detection by high-throughput DNA sequencing
homepage: https://github.com/yuchaojiang/CODEX2
version | versionsuffix | toolchain |
---|---|---|
20180227 |
-R-3.4.3 |
intel/2017b |
CodingQuarry¶
Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
homepage: https://sourceforge.net/p/codingquarry
version | toolchain |
---|---|
2.0 |
foss/2021b |
Cogent¶
Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.
homepage: https://github.com/Magdoll/Cogent
version | toolchain |
---|---|
8.0.0 |
foss/2021a |
Coin¶
Coin is an OpenGL-based, 3D graphics library that has its roots in the Open Inventor 2.1 API, which Coin still is compatible with.
homepage: https://coin3d.github.io
version | toolchain |
---|---|
4.0.0 |
GCC/10.3.0 , GCC/11.2.0 |
CoinUtils¶
CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.
homepage: https://github.com/coin-or/CoinUtils
version | toolchain |
---|---|
2.11.3 |
GCCcore/7.3.0 , foss/2018b |
2.11.4 |
GCC/10.3.0 , GCCcore/10.2.0 |
2.11.6 |
GCC/11.2.0 |
ColabFold¶
Making protein folding accessible to all. Predict proteins structures both in google colab and on your machine.
homepage: https://github.com/sokrypton/ColabFold
version | versionsuffix | toolchain |
---|---|---|
1.5.2 |
foss/2022a |
|
1.5.2 |
-CUDA-11.7.0 |
foss/2022a |
colossalai¶
Colossal-AI: A Unified Deep Learning System for Big Model Era
homepage: https://colossalai.org/
version | versionsuffix | toolchain |
---|---|---|
0.1.8 |
-CUDA-11.3.1 |
foss/2021a |
Commet¶
COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of a large metagenomic project.
homepage: https://colibread.inria.fr/software/commet/
version | versionsuffix | toolchain |
---|---|---|
20150415 |
-Python-2.7.11 |
foss/2016a |
CompareM¶
A toolbox for comparative genomics.
homepage: https://github.com/dparks1134/CompareM
version | versionsuffix | toolchain |
---|---|---|
0.0.23 |
-Python-2.7.15 |
foss/2018b |
0.1.2 |
foss/2021b |
Compress-Raw-Zlib¶
Low-Level Interface to zlib or zlib-ng compression library
homepage: https://metacpan.org/pod/Compress::Raw::Zlib
version | toolchain |
---|---|
2.202 |
GCCcore/11.3.0 |
COMSOL¶
COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems.
homepage: https://www.comsol.com
version | toolchain |
---|---|
5.4.0.225 |
system |
Con3F¶
Con3F is a Python package to read, manipulate and convert force field files
homepage: https://github.ugent.be/CMM/con3f
version | versionsuffix | toolchain |
---|---|---|
1.0-20190329 |
-Python-3.7.2 |
intel/2019a |
conan¶
Decentralized, open-source (MIT), C/C++ package manager.
homepage: https://conan.io
version | toolchain |
---|---|
1.58.0 |
GCCcore/11.3.0 |
CONCOCT¶
Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
homepage: https://concoct.readthedocs.io
version | versionsuffix | toolchain |
---|---|---|
1.0.0 |
-Python-2.7.14 |
foss/2017b |
1.0.0 |
-Python-2.7.15 |
foss/2018b |
1.0.0 |
-Python-3.6.3 |
foss/2017b |
1.1.0 |
-Python-2.7.15 |
foss/2019a |
1.1.0 |
-Python-2.7.18 |
foss/2020b |
configparser¶
configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5
homepage: https://docs.python.org/3/library/configparser.html
version | versionsuffix | toolchain |
---|---|---|
3.5.0 |
-Python-2.7.11 |
foss/2016a |
3.5.0 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
3.5.0 |
-Python-3.5.2 |
intel/2016b |
3.5.0 |
-Python-3.6.3 |
intel/2017b |
configurable-http-proxy¶
HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.
homepage: https://github.com/jupyterhub/configurable-http-proxy
version | versionsuffix | toolchain |
---|---|---|
1.3.0 |
-nodejs-4.4.7 |
foss/2016a |
3.1.1 |
-nodejs-8.9.4 |
foss/2017a |
4.2.1 |
GCCcore/10.2.0 |
|
4.4.0 |
GCCcore/10.3.0 |
|
4.5.3 |
GCCcore/11.3.0 |
CONN¶
CONN is an open-source Matlab/SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs.
homepage: https://web.conn-toolbox.org/home
version | versionsuffix | toolchain |
---|---|---|
21a |
-MATLAB-2021a |
system |
ConnectomeWorkbench¶
Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.
homepage: https://www.humanconnectome.org/software/connectome-workbench
version | versionsuffix | toolchain |
---|---|---|
1.2.2 |
system |
|
1.3.2 |
GCCcore/8.2.0 , foss/2017b , intel/2017b |
|
1.4.2 |
-rh_linux64 |
system |
1.5.0 |
GCCcore/10.3.0 |
Control-FREEC¶
Copy number and genotype annotation from whole genome and whole exome sequencing data.
homepage: https://github.com/BoevaLab/FREEC
version | toolchain |
---|---|
11.5 |
GCC/7.3.0-2.30 , GCC/8.2.0-2.31.1 |
11.6 |
GCC/10.2.0 |
cooler¶
Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices.
homepage: https://open2c.github.io/cooler
version | toolchain |
---|---|
0.9.1 |
foss/2022a |
CoordgenLibs¶
Schrodinger-developed 2D Coordinate Generation
homepage: https://github.com/schrodinger/coordgenlibs
version | toolchain |
---|---|
1.3.2 |
gompi/2019a , iimpi/2019a |
3.0.1 |
gompi/2019b , gompi/2021a , gompi/2022a , iimpi/2020a |
Coot¶
Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.
homepage: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot
version | versionsuffix | toolchain |
---|---|---|
0.8.1 |
-binary-Linux-x86_64-rhel-6-python-gtk2 |
system |
CopyKAT¶
CopyKAT: Inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data
homepage: https://github.com/navinlabcode/copykat
version | versionsuffix | toolchain |
---|---|---|
1.1.0 |
-R-4.2.1 |
foss/2022a |
core-counter¶
Tool to check available cores and OMP threads
homepage: https://github.com/gjbex/core-counter
version | toolchain |
---|---|
1.1.1 |
system |
Coreutils¶
The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.
homepage: https://www.gnu.org/software/coreutils/
version | toolchain |
---|---|
8.23 |
GCC/4.9.2 |
8.27 |
GCCcore/5.4.0 |
8.29 |
GCCcore/6.4.0 |
8.32 |
GCCcore/8.3.0 , GCCcore/9.3.0 |
9.0 |
GCCcore/11.2.0 |
corner¶
Make some beautiful corner plots.
homepage: https://corner.readthedocs.io/en/latest/
version | versionsuffix | toolchain |
---|---|---|
2.0.1 |
-Python-2.7.15 |
foss/2019a |
2.0.1 |
-Python-3.7.2 |
foss/2019a |
CoSymLib¶
Cosymlib is a python library for computing continuous symmetry & shape measures (CSMs & CShMs). Although its main aim is to provide simple and ready-to-use tools for the analysis of the symmetry & shape of molecules, many of the procedures contained in cosymlib can be easily applied to any finite geometrical object defined by a set of vertices or a by mass distribution function.
homepage: https://cosymlib.readthedocs.io
version | toolchain |
---|---|
0.10.9 |
foss/2022a |
coverage¶
Coverage.py is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not.
homepage: https://coverage.readthedocs.io
version | versionsuffix | toolchain |
---|---|---|
4.5.1 |
-Python-2.7.14 |
intel/2017b |
5.5 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
|
7.2.3 |
GCCcore/12.2.0 |
cowsay¶
Configurable talking characters in ASCII art
homepage: https://github.com/tnalpgge/rank-amateur-cowsay
version | toolchain |
---|---|
3.04 |
system |
CP2K¶
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
homepage: https://www.cp2k.org/
version | versionsuffix | toolchain |
---|---|---|
3.0 |
intel/2016a , intel/2016b , intel/2017b , intel/2018a |
|
3.0 |
-psmp |
intel/2016b |
4.1 |
intel/2016b |
|
4.1 |
-psmp |
foss/2016b |
5.1 |
foss/2018a , foss/2020a , foss/2020b , intel/2017b , intel/2018a , intel/2020a |
|
6.1 |
foss/2019a , intel/2018a , intel/2020a |
|
7.1 |
foss/2020a , foss/2020b , intel/2020a , intel/2020b |
|
7.1 |
-psmp |
foss/2020b |
8.1 |
foss/2020b |
|
8.2 |
foss/2021a , intel/2021a |
|
9.1 |
foss/2022a |
|
2022.1 |
foss/2022a |
CPB¶
CPB is a novel two-step Pearson correlation based biclustering approach to mine genes that are co-regulated with a given reference gene in order to discover genes that function in a common biological process. In the first step, the algorithm identifies subsets of genes with high correlation, reducing false negatives with a nonparametric filtering scheme. In the second step, biclusters from multiple datasets are used to extract and rank gene correlation information.
homepage: http://tda.gatech.edu/software/cpb/index.html
version | versionsuffix | toolchain |
---|---|---|
11-4-2011 |
-Python-2.7.13 |
foss/2017a |
CPC2¶
a fast and accurate coding potential calculator based on sequence intrinsic features
homepage: http://cpc2.gao-lab.org/
version | toolchain |
---|---|
1.0.1 |
foss/2022a |
CPLEX¶
IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability.
homepage: https://www.ibm.com/analytics/cplex-optimizer
version | versionsuffix | toolchain |
---|---|---|
12.9 |
GCCcore/8.2.0 |
|
12.10 |
-Python-3.7.4 |
GCCcore/8.3.0 |
22.1.1 |
GCCcore/11.2.0 |
CPPE¶
CPPE is an open-source, light-weight C++ and Python library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field (SCF) calculations and post-SCF methods. A convenient Python interface is also available.
homepage: https://github.com/maxscheurer/cppe
version | toolchain |
---|---|
0.3.1 |
GCC/11.3.0 |
CppUnit¶
CppUnit is the C++ port of the famous JUnit framework for unit testing.
homepage: https://freedesktop.org/wiki/Software/cppunit/
version | toolchain |
---|---|
1.12.1 |
GCCcore/6.4.0 , GCCcore/7.3.0 , foss/2016a |
1.15.1 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.3.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
cppy¶
A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.
homepage: https://github.com/nucleic/cppy
version | toolchain |
---|---|
1.1.0 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
1.2.1 |
GCCcore/11.3.0 , GCCcore/12.2.0 |
cppzmq¶
cppzmq is a C++ binding for libzmq.
homepage: https://github.com/zeromq/cppzmq
version | toolchain |
---|---|
4.9.0 |
system |
cpu_features¶
A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.
homepage: https://github.com/google/cpu_features
version | toolchain |
---|---|
0.6.0 |
GCCcore/10.2.0 |
cram¶
Cram is a functional testing framework for command line applications.
homepage: https://bitheap.org/cram
version | toolchain |
---|---|
0.7 |
GCCcore/8.2.0 |
cramtools¶
CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.
homepage: https://github.com/enasequence/cramtools/
version | versionsuffix | toolchain |
---|---|---|
2.0 |
-Java-1.7.0_80 |
system |
3.0 |
-Java-1.7.0_80 |
system |
CrayCCE¶
Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version | toolchain |
---|---|
19.06 |
system |
CrayGNU¶
Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version | toolchain |
---|---|
19.06 |
system |
CrayIntel¶
Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version | toolchain |
---|---|
19.06 |
system |
CrayPGI¶
Toolchain using Cray compiler wrapper, PrgEnv-pgi compiler (PE release: June 2019).
homepage: https://pubs.cray.com/discover
version | toolchain |
---|---|
19.06 |
system |
crb-blast¶
Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
homepage: https://github.com/cboursnell/crb-blast
version | versionsuffix | toolchain |
---|---|---|
0.6.9 |
gompi/2021a , gompi/2021b , intel/2017a |
|
0.6.9 |
-Ruby-2.6.1 |
foss/2018b |
CREST¶
CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles.
homepage: https://xtb-docs.readthedocs.io/en/latest/crest.html
version | toolchain |
---|---|
2.11 |
intel/2021a |
2.11.2 |
intel/2021a |
CRF++¶
CRF++ is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is designed for generic purpose and will be applied to a variety of NLP tasks, such as Named Entity Recognition, Information Extraction and Text Chunking.
homepage: https://taku910.github.io/crfpp/
version | toolchain |
---|---|
0.58 |
iccifort/2019.1.144-GCC-8.2.0-2.31.1 , intel/2018b |
CRISPR-DAV¶
CRISPR-DAV is a pipeline to analyze amplicon-based NGS data of CRISPR clones in a high throughput manner.
homepage: https://github.com/pinetree1/crispr-dav/
version | toolchain |
---|---|
2.3.4 |
foss/2020b |
CRISPResso2¶
CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.
homepage: https://github.com/pinellolab/CRISPResso2/
version | versionsuffix | toolchain |
---|---|---|
2.0.44 |
-Python-2.7.16 |
foss/2019b |
2.1.2 |
-Python-2.7.18 |
foss/2020b |
2.2.1 |
foss/2020b |
cromwell¶
Cromwell is a Workflow Management System geared towards scientific workflows.
homepage: http://cromwell.readthedocs.io/
version | versionsuffix | toolchain |
---|---|---|
56 |
-Java-11 |
system |
crossguid¶
CrossGuid is a minimal, cross platform, C++ GUID library. It uses the best native GUID/UUID generator on the given platform and has a generic class for parsing, stringifying, and comparing IDs. The guid generation technique is determined by your platform:
homepage: https://github.com/graeme-hill/crossguid
version | toolchain |
---|---|
20190529 |
GCCcore/11.3.0 |
CrossMap¶
CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF.
homepage: http://crossmap.sourceforge.net
version | versionsuffix | toolchain |
---|---|---|
0.3.9 |
-Python-3.7.2 |
foss/2019a |
CrossTalkZ¶
CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks.
homepage: http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/
version | toolchain |
---|---|
1.4 |
foss/2016a |
CRPropa¶
CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment.
homepage: https://crpropa.desy.de
version | versionsuffix | toolchain |
---|---|---|
3.1.5 |
-Python-3.7.2 |
foss/2019a |
3.1.6 |
-Python-3.8.2 |
foss/2020a |
Crumble¶
Exploration of controlled loss of quality values for compressing CRAM files
homepage: https://github.com/jkbonfield/crumble
version | toolchain |
---|---|
0.8.3 |
GCC/11.2.0 |
cryoCARE¶
This package is a memory efficient implementation of cryoCARE. This setup trains a denoising U-Net for tomographic reconstruction according to the Noise2Noise training paradigm. Therefore the user has to provide two tomograms of the same sample. The simplest way to achieve this is with direct- detector movie-frames. You can use Warp to generate two reconstructed tomograms based on the even/odd frames. Alternatively, the movie-frames can be split in two halves (e.g. with MotionCor2 -SplitSum 1 or with IMOD alignframes -debug 10000) from which two identical, up to random noise, tomograms can be reconstructed. These two (even and odd) tomograms can be used as input to this cryoCARE implementation.
homepage: https://github.com/juglab/cryoCARE_pip
version | versionsuffix | toolchain |
---|---|---|
0.2.1 |
-CUDA-11.3.1 |
foss/2021a |
cryoDRGN¶
cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction. CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.
homepage: https://cb.csail.mit.edu/cb/cryodrgn/
version | versionsuffix | toolchain |
---|---|---|
0.3.2 |
fosscuda/2020b |
|
0.3.5 |
-CUDA-11.3.1 |
foss/2021a |
1.0.0-beta |
-CUDA-11.3.1 |
foss/2021a |
CryptoMiniSat¶
CryptoMiniSat is an advanced SAT solver
homepage: https://github.com/msoos/cryptominisat
version | versionsuffix | toolchain |
---|---|---|
5.0.1 |
-Python-2.7.12 |
intel/2016b |
CrystFEL¶
CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.
homepage: http://www.desy.de/~twhite/crystfel/
version | toolchain |
---|---|
0.8.0 |
foss/2019a , intel/2019a |
CSB¶
Computational Structural Biology Toolbox CSB is a python library and application framework, which can be used to solve problems in the field of structural bioinformatics. If you are a bioinformatician, software engineer or a researcher working in this field, chances are you may find something useful here. Our package consists of a few major components: 1. Core class library - object-oriented, granular, with an emphasis on design and clean interfaces. 2. Application framework - console applications ("protocols"), which consume objects from the core library in order to build something executable (and hopefully useful). 3. Test framework - ensures that the library actually works.
homepage: https://github.com/csb-toolbox
version | toolchain |
---|---|
1.2.5 |
foss/2020b |
CSBDeep¶
CSBDeep is a toolbox for Content-aware Image Restoration (CARE).
homepage: https://csbdeep.bioimagecomputing.com/
version | versionsuffix | toolchain |
---|---|---|
0.4.1 |
-Python-3.7.2 |
foss/2019a , fosscuda/2019a |
CSBLAST¶
Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.
homepage: https://github.com/soedinglab/csblast/
version | toolchain |
---|---|
2.2.3 |
GCCcore/8.3.0 |
cscope¶
Cscope is a developer's tool for browsing source code.
homepage: http://cscope.sourceforge.net/
version | toolchain |
---|---|
15.9 |
system |
csvkit¶
csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.
homepage: https://github.com/wireservice/csvkit
version | versionsuffix | toolchain |
---|---|---|
1.0.4 |
GCCcore/8.2.0 |
|
1.0.5 |
-Python-3.7.4 |
GCCcore/8.3.0 |
1.1.0 |
GCCcore/11.3.0 |
ctags¶
Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.
homepage: http://ctags.sourceforge.net/
version | toolchain |
---|---|
5.8 |
system |
ctffind¶
Program for finding CTFs of electron micrographs.
homepage: https://grigoriefflab.umassmed.edu/ctffind4
version | versionsuffix | toolchain |
---|---|---|
4.1.13 |
foss/2019a , fosscuda/2019a , fosscuda/2019b |
|
4.1.14 |
foss/2019b , foss/2021b , foss/2022a , fosscuda/2019b , fosscuda/2020b |
|
4.1.14 |
-CUDA-11.3.1 |
foss/2021a |
CTPL¶
Modern and efficient C++ Thread Pool Library
homepage: https://github.com/vit-vit/CTPL.git
version | toolchain |
---|---|
0.0.2 |
GCC/11.3.0 |
Cube¶
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity.
homepage: http://www.scalasca.org/software/cube-4.x/download.html
version | toolchain |
---|---|
4.3.4 |
foss/2016a |
CubeGUI¶
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer.
homepage: https://www.scalasca.org/software/cube-4.x/download.html
version | toolchain |
---|---|
4.4.4 |
GCCcore/8.2.0 , GCCcore/9.3.0 |
4.6 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
4.8 |
GCCcore/11.3.0 |
CubeLib¶
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools.
homepage: https://www.scalasca.org/software/cube-4.x/download.html
version | toolchain |
---|---|
4.4.4 |
GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
4.6 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
4.8 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
CubeWriter¶
Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component.
homepage: https://www.scalasca.org/software/cube-4.x/download.html
version | toolchain |
---|---|
4.4.3 |
GCCcore/10.2.0 , GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
4.6 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
4.8 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
CUDA¶
CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
homepage: https://developer.nvidia.com/cuda-toolkit
version | toolchain |
---|---|
5.5.22 |
GCC/4.8.2 , system |
6.0.37 |
system |
6.5.14 |
system |
7.0.28 |
system |
7.5.18 |
GCC/4.9.4-2.25 , iccifort/2016.3.210-GCC-4.9.3-2.25 , system |
8.0.44 |
GCC/5.4.0-2.26 , iccifort/2016.3.210-GCC-5.4.0-2.26 , system |
8.0.61 |
system |
8.0.61_375.26 |
GCC/5.4.0-2.26 |
9.0.176 |
GCC/6.4.0-2.28 , iccifort/2017.4.196-GCC-6.4.0-2.28 , system |
9.1.85 |
GCC/6.4.0-2.28 , system |
9.2.88 |
GCC/6.4.0-2.28 , GCC/7.3.0-2.30 , system |
9.2.148.1 |
system |
10.0.130 |
system |
10.1.105 |
GCC/8.2.0-2.31.1 , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , system |
10.1.168 |
system |
10.1.243 |
GCC/8.3.0 , iccifort/2019.5.281 , system |
10.2.89 |
GCC/8.3.0 |
11.0.2 |
GCC/9.3.0 , iccifort/2020.1.217 |
11.1.1 |
GCC/10.2.0 , iccifort/2020.4.304 |
11.3.1 |
system |
11.4.1 |
system |
11.4.2 |
system |
11.5.0 |
system |
11.5.1 |
system |
11.5.2 |
system |
11.6.0 |
system |
11.7.0 |
system |
11.8.0 |
system |
12.0.0 |
system |
12.1.0 |
system |
CUDA-Samples¶
Samples for CUDA Developers which demonstrates features in CUDA Toolkit
homepage: https://github.com/NVIDIA/cuda-samples
version | versionsuffix | toolchain |
---|---|---|
11.3 |
-CUDA-11.3.1 |
GCC/10.3.0 |
CUDAcompat¶
Using the CUDA Forward Compatibility package, system administrators can run applications built using a newer toolkit even when an older driver that does not satisfy the minimum required driver version is installed on the system. This forward compatibility allows the CUDA deployments in data centers and enterprises to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit.
homepage: https://docs.nvidia.com/deploy/cuda-compatibility/index.html
version | versionsuffix | toolchain |
---|---|---|
11 |
system |
|
11.6 |
system |
|
11.6 |
-510.85.02 |
system |
11.7 |
system |
|
11.7 |
-515.65.01 |
system |
CUDAcore¶
CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
homepage: https://developer.nvidia.com/cuda-toolkit
version | toolchain |
---|---|
11.0.2 |
system |
11.1.1 |
system |
11.2.1 |
system |
11.2.2 |
system |
11.3.0 |
system |
11.4.0 |
system |
11.5.1 |
system |
cuDNN¶
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
homepage: https://developer.nvidia.com/cudnn
version | versionsuffix | toolchain |
---|---|---|
4.0 |
system |
|
5.0 |
-CUDA-7.5.18 |
system |
5.0-rc |
system |
|
5.1 |
-CUDA-8.0.44 |
system |
6.0 |
-CUDA-8.0.61 |
system |
6.0.21 |
-CUDA-7.5.18 |
system |
6.0.21 |
-CUDA-8.0.44 |
system |
7.0.2 |
-CUDA-9.0.176 |
system |
7.0.5 |
-CUDA-8.0.44 |
system |
7.0.5 |
-CUDA-9.0.176 |
system |
7.0.5 |
-CUDA-9.1.85 |
system |
7.0.5.15 |
fosscuda/2017b , fosscuda/2018a , intelcuda/2017b |
|
7.1.4.18 |
fosscuda/2018b |
|
7.4.2.24 |
gcccuda/2019a |
|
7.4.2.24 |
-CUDA-10.0.130 |
system |
7.5.0.56 |
-CUDA-10.0.130 |
system |
7.6.2.24 |
-CUDA-10.1.243 |
system |
7.6.4.38 |
gcccuda/2019a , gcccuda/2019b |
|
7.6.4.38 |
-CUDA-10.0.130 |
system |
8.0.4.30 |
-CUDA-11.0.2 |
system |
8.0.4.30 |
-CUDA-11.1.1 |
system |
8.0.5.39 |
-CUDA-11.1.1 |
system |
8.1.0.77 |
-CUDA-11.2.1 |
system |
8.1.1.33 |
-CUDA-11.2.1 |
system |
8.2.1.32 |
-CUDA-11.3.1 |
system |
8.2.2.26 |
-CUDA-11.4.0 |
system |
8.2.2.26 |
-CUDA-11.4.1 |
system |
8.4.0.27 |
-CUDA-11.6.0 |
system |
8.4.1.50 |
-CUDA-11.5.2 |
system |
8.4.1.50 |
-CUDA-11.6.0 |
system |
8.4.1.50 |
-CUDA-11.7.0 |
system |
8.6.0.163 |
-CUDA-11.8.0 |
system |
8.7.0.84 |
-CUDA-11.8.0 |
system |
8.8.0.121 |
-CUDA-12.0.0 |
system |
Cufflinks¶
Transcript assembly, differential expression, and differential regulation for RNA-Seq
homepage: http://cole-trapnell-lab.github.io/cufflinks/
version | toolchain |
---|---|
2.2.1 |
foss/2016a , foss/2016b , foss/2018b , gompi/2019b , intel/2017b , intel/2018a |
20190706 |
GCC/10.2.0 , GCC/11.2.0 , gompi/2019a |
CUnit¶
Automated testing framework for C.
homepage: https://sourceforge.net/projects/cunit/
version | toolchain |
---|---|
2.1-3 |
GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/6.4.0 |
CuPy¶
CuPy is an open-source array library accelerated with NVIDIA CUDA.
homepage: https://cupy.dev
version | versionsuffix | toolchain |
---|---|---|
8.2.0 |
-Python-3.7.4 |
fosscuda/2019b |
8.5.0 |
fosscuda/2020b |
|
11.4.0 |
-CUDA-11.4.1 |
foss/2021b |
cURL¶
libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
homepage: https://curl.haxx.se
version | toolchain |
---|---|
7.33.0 |
GCC/4.8.2 |
7.34.0 |
GCC/4.8.2 |
7.40.0 |
GCC/4.9.2 |
7.46.0 |
iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 |
7.47.0 |
foss/2016a , intel/2016.02-GCC-4.9 , intel/2016a |
7.49.1 |
GCCcore/5.4.0 , foss/2016a , foss/2016b , intel/2016a , intel/2016b |
7.52.1 |
gimkl/2017a , intel/2016b |
7.53.1 |
GCCcore/6.3.0 |
7.54.0 |
GCCcore/6.3.0 |
7.55.1 |
GCCcore/6.4.0 |
7.56.0 |
GCCcore/6.4.0 |
7.56.1 |
GCCcore/6.4.0 |
7.58.0 |
GCCcore/6.4.0 |
7.59.0 |
GCCcore/6.4.0 |
7.60.0 |
GCCcore/7.2.0 , GCCcore/7.3.0 |
7.63.0 |
GCCcore/8.2.0 |
7.66.0 |
GCCcore/8.3.0 |
7.69.1 |
GCCcore/9.3.0 |
7.72.0 |
GCCcore/10.2.0 |
7.76.0 |
GCCcore/10.3.0 |
7.78.0 |
GCCcore/11.2.0 |
7.83.0 |
GCCcore/11.3.0 |
7.84.0 |
GCCcore/12.1.0 |
7.86.0 |
GCCcore/12.2.0 |
8.0.1 |
GCCcore/12.3.0 , GCCcore/13.1.0 |
cuSPARSELt¶
NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix
homepage: https://docs.nvidia.com/cuda/cusparselt/index.html
version | versionsuffix | toolchain |
---|---|---|
0.3.0.3 |
-CUDA-11.4.1 |
system |
custodian¶
A simple JIT job management framework in Python.
homepage: https://pypi.python.org/pypi/custodian
version | versionsuffix | toolchain |
---|---|---|
1.1.0 |
-Python-2.7.13 |
intel/2017a |
cutadapt¶
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
homepage: https://opensource.scilifelab.se/projects/cutadapt/
version | versionsuffix | toolchain |
---|---|---|
1.9.1 |
-Python-2.7.11 |
foss/2016a |
1.9.1 |
-Python-2.7.12 |
foss/2016b |
1.14 |
-Python-2.7.13 |
foss/2017a , intel/2017a |
1.15 |
-Python-3.5.2 |
foss/2016b |
1.16 |
-Python-2.7.14 |
foss/2017b , intel/2017b , intel/2018a |
1.16 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
1.16 |
-Python-3.6.4 |
foss/2018a , intel/2018a |
1.18 |
GCCcore/8.2.0 , GCCcore/8.3.0 |
|
1.18 |
-Python-2.7.15 |
foss/2018b |
1.18 |
-Python-2.7.18 |
GCC/10.2.0 |
1.18 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
2.1 |
-Python-3.6.6 |
foss/2018b |
2.7 |
-Python-3.7.4 |
GCCcore/8.3.0 |
2.8 |
-Python-3.7.4 |
GCCcore/8.3.0 |
2.10 |
-Python-3.7.4 |
GCCcore/8.3.0 |
2.10 |
-Python-3.8.2 |
GCCcore/9.3.0 |
3.4 |
GCCcore/10.2.0 , GCCcore/10.3.0 |
|
3.5 |
GCCcore/11.2.0 |
|
4.2 |
GCCcore/11.3.0 |
cuTENSOR¶
The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations.
homepage: https://developer.nvidia.com/cutensor
version | versionsuffix | toolchain |
---|---|---|
1.2.2.5 |
gcccuda/2019b |
|
1.2.2.5 |
-CUDA-11.1.1 |
system |
1.6.0.3 |
-CUDA-11.3.1 |
system |
1.6.1.5 |
-CUDA-11.4.1 |
system |
1.6.1.5 |
-CUDA-11.7.0 |
system |
CVS¶
CVS is a version control system, an important component of Source Configuration Management (SCM).
homepage: https://savannah.nongnu.org/projects/cvs
version | toolchain |
---|---|
1.11.23 |
GCC/4.8.2 , GCCcore/11.2.0 , GCCcore/4.9.3 , GCCcore/6.4.0 |
CVXOPT¶
CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language.
homepage: https://cvxopt.org
version | versionsuffix | toolchain |
---|---|---|
1.1.9 |
-Python-2.7.13 |
intel/2017a |
1.2.1 |
-Python-3.6.4 |
intel/2018a |
1.2.3 |
foss/2019a |
|
1.2.3 |
-Python-3.6.6 |
intel/2018b |
1.2.4 |
-Python-3.7.4 |
intel/2019b |
1.2.6 |
foss/2020b , foss/2021a |
CVXPY¶
CVXPY is a Python-embedded modeling language for convex optimization problems. It allows you to express your problem in a natural way that follows the math, rather than in the restrictive standard form required by solvers.
homepage: https://www.cvxpy.org/
version | versionsuffix | toolchain |
---|---|---|
1.0.24 |
foss/2019a |
|
1.0.28 |
-Python-3.7.4 |
foss/2019b |
CWIPI¶
CWIPI (Coupling With Interpolation Parallel Interface) library helps in chaining and coupling codes. Provides exchanges of interpolated fields through a non-compliant geometric interface and allows control of the coupling algorithm using control parameters. CWIPI takes advantage of the distribution of the definition of the coupling algorithm in the different codes.
homepage: https://w3.onera.fr/cwipi/
version | toolchain |
---|---|
0.12.0 |
gompi/2021a |
cwltool¶
Common workflow language (CWL) reference implementation.
homepage: https://github.com/common-workflow-language/cwltool
version | toolchain |
---|---|
3.1.20221008225030 |
foss/2021a |
3.1.20221018083734 |
foss/2021a |
cxxopts¶
cxxopts is a lightweight C++ command line option parser
homepage: https://github.com/jarro2783/cxxopts
version | toolchain |
---|---|
3.0.0 |
system |
cysignals¶
The cysignals package provides mechanisms to handle interrupts (and other signals and errors) in Cython code.
homepage: https://pypi.org/project/cysignals/
version | versionsuffix | toolchain |
---|---|---|
1.10.2 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
1.10.2 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
Cython¶
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
homepage: https://cython.org/
version | versionsuffix | toolchain |
---|---|---|
0.23.4 |
-Python-2.7.10 |
gimkl/2.11.5 |
0.24.1 |
-Python-2.7.11 |
foss/2016a |
0.25.2 |
-Python-2.7.12 |
foss/2016b |
0.25.2 |
-Python-3.6.4 |
intel/2018a |
0.27.3 |
-Python-2.7.15 |
GCCcore/8.2.0 |
0.29.10 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
0.29.10 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
0.29.22 |
GCCcore/10.2.0 |
|
0.29.33 |
GCCcore/11.3.0 |
|
3.0a5 |
GCCcore/10.2.0 |
cython-blis¶
Fast BLAS-like operations from Python and Cython, without the tears. Provides the Blis linear algebra routines as a self-contained Python C-extension.
homepage: https://github.com/explosion/cython-blis
version | toolchain |
---|---|
0.9.1 |
foss/2022a |
cytoolz¶
Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries.
homepage: https://github.com/pytoolz/cytoolz
version | versionsuffix | toolchain |
---|---|---|
0.10.1 |
-Python-3.6.6 |
foss/2018b |
0.10.1 |
-Python-3.7.2 |
GCCcore/8.2.0 |
Cytoscape¶
Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
homepage: https://cytoscape.org/
version | versionsuffix | toolchain |
---|---|---|
3.9.1 |
-Java-11 |
system |
cytosim¶
Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).
homepage: https://github.com/nedelec/cytosim
version | versionsuffix | toolchain |
---|---|---|
20190117 |
-mkl |
gomkl/2019a |
cyvcf2¶
cython + htslib == fast VCF and BCF processing
homepage: https://github.com/brentp/cyvcf2
version | versionsuffix | toolchain |
---|---|---|
0.10.10 |
-Python-3.6.6 |
foss/2018b |
0.11.5 |
foss/2019a , intel/2019a |
D¶
dadi - dagitty - Dakota - Dalton - damageproto - dammit - DANPOS2 - DAS_Tool - dask - dask-labextension - datamash - davix - DB - DB_File - DBCSR - DBD-mysql - DBG2OLC - DBus - dbus-glib - dclone - dcm2niix - DCMTK - dd - deal.II - deap - decona - deconf - DeconICA - deepdiff - DeepLabCut - deepmedic - DeepMod2 - DeepSurv - deepTools - Delly - DeMixT - DendroPy - DensPart - Deprecated - destiny - Detectron2 - detonate - Devito - DFA - DFT-D3 - DFT-D4 - DFTB+ - dftd3-lib - DGL - DIAL - DIALOGUE - DIAMOND - Dice - DiCE-ML - dicom2nifti - DicomBrowser - Diffutils - dijitso - dill - DIRAC - distributed - DistributedStream - DL_POLY_4 - DL_POLY_Classic - dlb - dlib - DLPack - dm-reverb - dm-tree - DMCfun - DMLC-Core - DMTCP - DOLFIN - dorado - Doris - DosageConvertor - dotNET-Core-Runtime - dotNET-SDK - double-conversion - DoubletFinder - Doxygen - DRAGMAP - Drake - dRep - DROP - dropEst - DSA - dSFMT - DSRC - Dsuite - dtcmp - dtcwt - DualSPHysics - DUBStepR - dune-core - dune-fem - duplex-tools - dxpy - DyMat
dadi¶
∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum.
homepage: https://bitbucket.org/gutenkunstlab/dadi
version | versionsuffix | toolchain |
---|---|---|
1.7.0 |
-Python-2.7.12 |
intel/2016b |
dagitty¶
A port of the web-based software 'DAGitty', available at http://dagitty.net, for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation.
homepage: https://cran.r-project.org/web/packages/dagitty/
version | versionsuffix | toolchain |
---|---|---|
0.2-2 |
-R-3.5.1 |
foss/2018b |
Dakota¶
The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models.
homepage: https://dakota.sandia.gov/
version | toolchain |
---|---|
6.16.0 |
foss/2021b |
Dalton¶
The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html.
homepage: https://daltonprogram.org/
version | versionsuffix | toolchain |
---|---|---|
2016 |
-i8 |
intel/2017b |
2020.0 |
foss/2021a |
damageproto¶
X protocol and ancillary headers for xinerama
homepage: http://www.freedesktop.org/wiki/Software/xlibs
version | toolchain |
---|---|
1.2.1 |
foss/2016a , intel/2016a |
dammit¶
dammit is a simple de novo transcriptome annotator. It was born out of the observations that annotation is mundane and annoying, all the individual pieces of the process exist already, and the existing solutions are overly complicated or rely on crappy non-free software.
homepage: http://www.camillescott.org/dammit/
version | versionsuffix | toolchain |
---|---|---|
0.3.2 |
-Python-2.7.13 |
intel/2017a |
DANPOS2¶
A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2
homepage: https://sites.google.com/site/danposdoc
version | versionsuffix | toolchain |
---|---|---|
2.2.2 |
-Python-2.7.12 |
foss/2016b |
DAS_Tool¶
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
homepage: https://github.com/cmks/DAS_Tool
version | versionsuffix | toolchain |
---|---|---|
1.1.1 |
-R-3.5.1-Python-2.7.15 |
foss/2018b |
1.1.1 |
-R-4.1.2 |
foss/2021b |
1.1.3 |
-R-4.1.0 |
foss/2021a |
dask¶
Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
homepage: https://dask.org/
version | versionsuffix | toolchain |
---|---|---|
0.8.2 |
-Python-2.7.11 |
intel/2016a |
0.8.2 |
-Python-3.5.1 |
intel/2016a |
0.11.0 |
-Python-2.7.11 |
foss/2016a |
0.11.0 |
-Python-2.7.12 |
intel/2016b |
0.11.0 |
-Python-3.5.2 |
intel/2016b |
0.12.0 |
-Python-2.7.12 |
intel/2016b |
0.12.0 |
-Python-3.5.2 |
foss/2016b , intel/2016b |
0.16.0 |
-Python-2.7.14 |
foss/2017b , intel/2017b |
0.16.0 |
-Python-3.6.3 |
foss/2017b , intel/2017b |
0.17.0 |
-Python-2.7.13 |
foss/2017a , intel/2017a |
0.17.0 |
-Python-3.6.1 |
intel/2017a |
0.17.2 |
-Python-3.6.4 |
foss/2018a , intel/2018a |
0.19.4 |
-Python-3.6.6 |
foss/2018b , fosscuda/2018b , intel/2018b |
1.0.0 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
1.1.4 |
-Python-2.7.15 |
fosscuda/2018b |
2.3.0 |
-Python-3.7.2 |
foss/2019a |
2.8.0 |
-Python-3.7.4 |
foss/2019b , fosscuda/2019b , intel/2019b |
2.18.1 |
-Python-3.8.2 |
foss/2020a , intel/2020a |
2021.2.0 |
foss/2020b , fosscuda/2020b , intel/2020b , intelcuda/2020b |
|
2021.9.1 |
foss/2021a |
|
2022.1.0 |
foss/2021b |
|
2022.10.0 |
foss/2022a |
dask-labextension¶
This package provides a JupyterLab extension to manage Dask clusters, as well as embed Dask's dashboard plots directly into JupyterLab panes.
homepage: https://github.com/dask/dask-labextension
version | toolchain |
---|---|
6.0.0 |
foss/2022a |
datamash¶
GNU datamash performs basic numeric, textual and statistical operations on input data files
homepage: https://www.gnu.org/software/datamash/
version | toolchain |
---|---|
1.3 |
foss/2018a |
1.5 |
GCCcore/10.2.0 , GCCcore/7.3.0 , GCCcore/8.3.0 |
davix¶
The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols.
homepage: https://dmc.web.cern.ch/projects/davix/home
version | toolchain |
---|---|
0.6.6 |
intel/2017a |
0.7.5 |
GCCcore/8.3.0 |
DB¶
Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
homepage: http://www.oracle.com/technetwork/products/berkeleydb
version | toolchain |
---|---|
4.8.30 |
intel/2016a |
6.2.23 |
foss/2016a |
6.2.32 |
GCCcore/6.4.0 , intel/2017a |
18.1.25 |
GCCcore/7.3.0 |
18.1.32 |
GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.3.0 |
18.1.40 |
FCC/4.5.0 , GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/12.1.0 , GCCcore/12.2.0 , GCCcore/12.3.0 , GCCcore/8.2.0 , GCCcore/8.3.0 |
DB_File¶
Perl5 access to Berkeley DB version 1.x.
homepage: https://perldoc.perl.org/DB_File.html
version | versionsuffix | toolchain |
---|---|---|
1.835 |
GCCcore/9.3.0 |
|
1.835 |
-Perl-5.20.3 |
intel/2016a |
1.835 |
-Perl-5.22.1 |
foss/2016a |
1.855 |
GCCcore/10.2.0 |
|
1.856 |
GCCcore/10.3.0 |
|
1.857 |
GCCcore/11.2.0 |
|
1.858 |
GCCcore/11.3.0 |
DBCSR¶
DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations.
homepage: https://cp2k.github.io/dbcsr/develop/
version | toolchain |
---|---|
2.5.0 |
foss/2021b |
DBD-mysql¶
Perl binding for MySQL
homepage: https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm
version | versionsuffix | toolchain |
---|---|---|
4.032 |
-Perl-5.22.2 |
intel/2016a |
4.033 |
-Perl-5.24.0 |
intel/2016b |
4.042 |
-Perl-5.24.1 |
intel/2017a |
4.046 |
-Perl-5.26.0 |
foss/2017b , intel/2017b |
4.046 |
-Perl-5.26.1 |
intel/2018a |
4.048 |
-Perl-5.28.0 |
foss/2018b |
4.050 |
GCC/10.2.0 , GCC/11.2.0 , GCC/11.3.0 |
|
4.050 |
-Perl-5.28.1 |
foss/2019a |
DBG2OLC¶
DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
homepage: https://github.com/yechengxi/DBG2OLC
version | toolchain |
---|---|
20170208 |
intel/2016b , intel/2017a |
20180221 |
GCC/6.4.0-2.28 , iccifort/2017.4.196-GCC-6.4.0-2.28 |
20200724 |
GCC/11.3.0 |
DBus¶
D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.
homepage: https://dbus.freedesktop.org/
version | toolchain |
---|---|
1.10.8 |
foss/2016a , intel/2016a |
1.10.12 |
intel/2016b |
1.10.20 |
GCCcore/6.4.0 |
1.11.20 |
intel/2017a |
1.13.0 |
intel/2017b |
1.13.6 |
GCCcore/6.4.0 , GCCcore/7.3.0 |
1.13.8 |
GCCcore/8.2.0 |
1.13.12 |
GCCcore/8.3.0 , GCCcore/9.3.0 |
1.13.18 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 |
1.14.0 |
GCCcore/11.3.0 |
1.15.2 |
GCCcore/12.2.0 |
1.15.4 |
GCCcore/12.3.0 |
dbus-glib¶
D-Bus is a message bus system, a simple way for applications to talk to one another.
homepage: https://dbus.freedesktop.org/doc/dbus-glib
version | toolchain |
---|---|
0.106 |
foss/2016a , intel/2016a |
0.108 |
intel/2016b , intel/2017a |
0.110 |
GCCcore/7.3.0 , GCCcore/8.2.0 , GCCcore/8.3.0 , intel/2017b |
0.112 |
GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 |
dclone¶
Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods
homepage: https://cran.r-project.org/web/packages/dclone
version | versionsuffix | toolchain |
---|---|---|
2.3-0 |
-R-4.2.1 |
foss/2022a |
dcm2niix¶
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.
homepage: https://github.com/rordenlab/dcm2niix
version | toolchain |
---|---|
1.0.20180622 |
GCCcore/6.4.0 , GCCcore/7.3.0 |
1.0.20190902 |
GCCcore/7.3.0 , GCCcore/8.2.0 |
1.0.20200331 |
GCCcore/8.3.0 |
1.0.20201102 |
GCCcore/8.3.0 |
1.0.20211006 |
GCCcore/10.3.0 |
1.0.20220720 |
GCCcore/11.3.0 |
DCMTK¶
DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.
homepage: https://dicom.offis.de/dcmtk
version | toolchain |
---|---|
3.6.3 |
GCCcore/7.3.0 |
3.6.5 |
GCCcore/8.2.0 , GCCcore/8.3.0 |
3.6.6 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
3.6.7 |
GCCcore/11.3.0 |
dd¶
dd is a package for working with binary decision diagrams that includes both a pure Python implementation and Cython bindings to C libraries (CUDD, Sylvan, BuDDy). The Python and Cython modules implement the same API, so the same user code runs with both. All the standard operations on BDDs are available, including dynamic variable reordering using sifting, garbage collection, dump/load from files, plotting, and a parser of quantified Boolean expressions. This module includes bindings for: CUDD v3.0.0, Sylvan v1.0.0
homepage: https://github.com/tulip-control/dd
version | versionsuffix | toolchain |
---|---|---|
0.5.6 |
-Python-3.8.2 |
foss/2020a |
deal.II¶
deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.
homepage: https://www.dealii.org
version | toolchain |
---|---|
9.1.1 |
foss/2019a , intel/2019a |
9.3.3 |
foss/2021a |
deap¶
DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent.
homepage: http://deap.readthedocs.org/en/master/
version | versionsuffix | toolchain |
---|---|---|
0.9.2 |
-Python-2.7.12 |
intel/2016b |
decona¶
fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
homepage: https://github.com/Saskia-Oosterbroek/decona
version | versionsuffix | toolchain |
---|---|---|
0.1.2 |
-Python-3.7.4 |
foss/2019b |
deconf¶
decomposition (deconfounding) of OMICS datasets in heterogeneous tissues
homepage: http://web.cbio.uct.ac.za/~renaud/CRAN/
version | versionsuffix | toolchain |
---|---|---|
1.0.1 |
-R-3.5.1 |
foss/2018b |
DeconICA¶
Deconvolution of transcriptome through Immune Component Analysis (DeconICA) is an R package for identifying immune-related signals in transcriptome through deconvolution or unsupervised source separation methods.
homepage: https://urszulaczerwinska.github.io/DeconICA
version | versionsuffix | toolchain |
---|---|---|
0.1.0 |
-R-3.5.1 |
foss/2018b |
deepdiff¶
DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.
homepage: https://zepworks.com/deepdiff/current/
version | versionsuffix | toolchain |
---|---|---|
3.3.0 |
-Python-2.7.15 |
intel/2018b |
3.3.0 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
4.0.6 |
-Python-3.7.2 |
GCCcore/8.2.0 |
5.0.2 |
-Python-3.7.4 |
GCCcore/8.3.0 |
5.7.0 |
GCCcore/11.2.0 |
|
5.8.1 |
GCCcore/11.3.0 |
DeepLabCut¶
Markerless tracking of user-defined features with deep learning
homepage: http://www.mousemotorlab.org/deeplabcut
version | versionsuffix | toolchain |
---|---|---|
2.2.0.6 |
-CUDA-11.3.1 |
foss/2021a |
deepmedic¶
Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans.
homepage: https://biomedia.doc.ic.ac.uk/software/deepmedic/
version | versionsuffix | toolchain |
---|---|---|
0.8.2 |
foss/2021a |
|
0.8.2 |
-CUDA-11.3.1 |
foss/2021a |
DeepMod2¶
DeepMod2 is a computational tool for detecting DNA methylation and modifications from Oxford Nanopore reads.
homepage: https://github.com/WGLab/DeepMod2
version | toolchain |
---|---|
0.0.1 |
foss/2021a |
DeepSurv¶
DeepSurv is a deep learning approach to survival analysis.
homepage: https://github.com/jaredleekatzman/DeepSurv
version | versionsuffix | toolchain |
---|---|---|
2.0.0-20180922 |
-Python-3.6.6 |
fosscuda/2018b |
deepTools¶
deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
homepage: https://deeptools.readthedocs.io/
version | versionsuffix | toolchain |
---|---|---|
2.5.4 |
-Python-3.6.3 |
intel/2017b |
3.3.1 |
-Python-3.6.6 |
foss/2018b |
3.3.1 |
-Python-3.7.4 |
intel/2019b |
3.3.1 |
-Python-3.8.2 |
foss/2020a |
3.5.0 |
foss/2021a |
|
3.5.1 |
foss/2021b |
Delly¶
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
homepage: https://github.com/dellytools/delly/
version | versionsuffix | toolchain |
---|---|---|
0.7.8 |
-linux_x86_64 |
system |
0.8.7 |
gompi/2020b |
|
1.1.5 |
GCC/11.3.0 |
DeMixT¶
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms.
homepage: https://bioinformatics.mdanderson.org/main/DeMixT
version | versionsuffix | toolchain |
---|---|---|
0.2.1 |
-R-3.5.1 |
foss/2018b |
DendroPy¶
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
homepage: https://dendropy.org/
version | versionsuffix | toolchain |
---|---|---|
4.4.0 |
GCCcore/8.2.0 , GCCcore/8.3.0 , GCCcore/9.3.0 , intel/2019a |
|
4.4.0 |
-Python-2.7.15 |
intel/2018b |
4.5.2 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/11.3.0 |
|
4.5.2 |
-Python-2.7.18 |
GCCcore/10.2.0 |
DensPart¶
Atoms-in-molecules density partitioning schemes based on stockholder recipe
homepage: https://github.com/theochem/denspart
version | toolchain |
---|---|
20220603 |
intel/2022a |
Deprecated¶
If you need to mark a function or a method as deprecated, you can use the @deprecated decorator.
homepage: https://github.com/tantale/deprecated
version | toolchain |
---|---|
1.2.13 |
foss/2021a , foss/2022a |
destiny¶
R packages to create and plot diffusion maps.
homepage: https://bioconductor.org/packages/destiny
version | versionsuffix | toolchain |
---|---|---|
2.5.6 |
-R-3.4.0 |
intel/2017a |
Detectron2¶
Detectron2 is Facebook AI Research's next generation library that provides state-of-the-art detection and segmentation algorithms. It is the successor of Detectron and maskrcnn-benchmark. It supports a number of computer vision research projects and production applications in Facebook.
homepage: https://github.com/facebookresearch/detectron2
version | versionsuffix | toolchain |
---|---|---|
0.6 |
foss/2021a |
|
0.6 |
-CUDA-11.3.1 |
foss/2021a |
detonate¶
DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
homepage: http://deweylab.biostat.wisc.edu/detonate/
version | toolchain |
---|---|
1.11 |
intel/2017b |
Devito¶
Devito is a domain-specific Language (DSL) and code generation framework for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on multiple computer platforms.
homepage: https://www.devitoproject.org
version | versionsuffix | toolchain |
---|---|---|
4.6.1 |
-Python-3.8.2 |
foss/2020a |
DFA¶
Python library for modeling DFAs, Moore Machines, and Transition Systems.
homepage: https://github.com/mvcisback/dfa
version | versionsuffix | toolchain |
---|---|---|
0.3.4 |
-Python-3.8.2 |
GCCcore/9.3.0 |
2.1.2 |
GCCcore/10.2.0 |
DFT-D3¶
DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.
homepage: https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3
version | toolchain |
---|---|
3.2.0 |
GCC/8.3.0 , iccifort/2020.4.304 , intel-compilers/2021.2.0 , intel-compilers/2021.4.0 , intel/2019a |
DFT-D4¶
Generally Applicable Atomic-Charge Dependent London Dispersion Correction.
homepage: https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4
version | versionsuffix | toolchain |
---|---|---|
3.2.0 |
-Python-3.7.4 |
intel/2019b |
DFTB+¶
DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed.
homepage: https://www.dftb-plus.info
version | versionsuffix | toolchain |
---|---|---|
1.3.1 |
intel/2017a |
|
17.1 |
-Python-2.7.14 |
intel/2017b |
19.1 |
-Python-2.7.16 |
foss/2019b |
19.1 |
-Python-2.7.16-mpi |
foss/2019b |
21.1 |
intel/2021a |
dftd3-lib¶
This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.
homepage: https://github.com/dftbplus/dftd3-lib
version | toolchain |
---|---|
0.9 |
GCC/8.3.0 , intel-compilers/2021.2.0 |
DGL¶
DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.
homepage: https://www.dgl.ai
version | versionsuffix | toolchain |
---|---|---|
0.6.1 |
-Python-3.7.4-PyTorch-1.8.1 |
fosscuda/2019b |
0.9.1 |
-CUDA-11.3.1 |
foss/2021a |
DIAL¶
DIAL (De novo Identification of Alleles) is a collection of programs to automate the discovery of alleles for a species where we lack a reference sequence. The SNPs/alleles are specifically selected for a low error rate in genotyping assays.
homepage: http://www.bx.psu.edu/miller_lab/
version | toolchain |
---|---|
2011.06.06 |
foss/2016a |
DIALOGUE¶
DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.
homepage: https://github.com/livnatje/DIALOGUE
version | versionsuffix | toolchain |
---|---|---|
1.0-20230228 |
-R-4.2.0 |
foss/2021b |
DIAMOND¶
Accelerated BLAST compatible local sequence aligner
homepage: https://github.com/bbuchfink/diamond
version | toolchain |
---|---|
0.9.22 |
foss/2018a , foss/2018b , intel/2018a , intel/2018b |
0.9.24 |
iccifort/2019.1.144-GCC-8.2.0-2.31.1 |
0.9.30 |
GCC/8.3.0 , iccifort/2019.5.281 |
0.9.36 |
GCC/9.3.0 |
2.0.4 |
GCC/9.3.0 |
2.0.6 |
GCC/7.3.0-2.30 |
2.0.7 |
GCC/10.2.0 |
2.0.11 |
GCC/10.3.0 |
2.0.13 |
GCC/10.3.0 , GCC/11.2.0 |
2.1.0 |
GCC/11.3.0 |
Dice¶
Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems.
homepage: https://github.com/sanshar/Dice
version | toolchain |
---|---|
20221025 |
foss/2022a |
DiCE-ML¶
Diverse Counterfactual Explanations (DiCE) for ML
homepage: https://interpret.ml/DiCE
version | toolchain |
---|---|
0.9 |
foss/2022a |
dicom2nifti¶
Python library for converting dicom files to nifti
homepage: https://github.com/icometrix/dicom2nifti
version | versionsuffix | toolchain |
---|---|---|
2.2.12 |
-Python-3.8.2 |
foss/2020a |
2.3.0 |
foss/2020b |
DicomBrowser¶
DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once.
homepage: http://nrg.wustl.edu/software/dicom-browser/
version | versionsuffix | toolchain |
---|---|---|
1.7.0b5 |
-Java-1.7.0_80 |
system |
Diffutils¶
Diffutils: GNU diff utilities - find the differences between files
homepage: http://www.gnu.org/software/diffutils/diffutils.html
version | toolchain |
---|---|
3.3 |
GCC/4.8.2 |
dijitso¶
dijitso is a Python module for distributed just-in-time shared library building.
homepage: https://bitbucket.org/fenics-project/dijitso
version | versionsuffix | toolchain |
---|---|---|
2019.1.0 |
-Python-3.7.4 |
foss/2019b |
dill¶
dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy.
homepage: https://pypi.org/project/dill/
version | toolchain |
---|---|
0.3.0 |
GCCcore/8.2.0 |
0.3.3 |
GCCcore/10.2.0 , GCCcore/8.3.0 |
0.3.4 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
0.3.6 |
GCCcore/11.3.0 |
DIRAC¶
DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations
homepage: http://www.diracprogram.org
version | versionsuffix | toolchain |
---|---|---|
19.0 |
-Python-2.7.18-int64 |
intel/2020a |
19.0 |
-Python-2.7.18-mpi-int64 |
intel/2020a |
22.0 |
foss/2021a , intel/2021a |
|
22.0 |
-int64 |
intel/2021a |
23.0 |
foss/2022b , intel/2022b |
|
23.0 |
-int64 |
intel/2022b |
distributed¶
Dask.distributed is a lightweight library for distributed computing in Python. It extends both the concurrent.futures and dask APIs to moderate sized clusters.
homepage: https://distributed.readthedocs.io/
version | versionsuffix | toolchain |
---|---|---|
1.14.3 |
-Python-2.7.12 |
intel/2016b |
1.14.3 |
-Python-3.5.2 |
intel/2016b |
1.21.6 |
-Python-3.6.4 |
intel/2018a |
DistributedStream¶
A MPI distributed stream benchmark, useful to identifying nodes with poor memory performance and characterising memory bandwidth variation over systems.
homepage: https://github.com/adrianjhpc/DistributedStream
version | toolchain |
---|---|
1.0 |
gompi/2021a |
DL_POLY_4¶
DL_POLY is a general purpose classical molecular dynamics (MD) simulation software
homepage: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx
version | toolchain |
---|---|
5.0.0 |
foss/2020b , intel/2020b |
DL_POLY_Classic¶
DL_POLY Classic is a freely available molecular dynamics program developed from the DL_POLY_2 package. This version does not install the java gui.
homepage: http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/
version | versionsuffix | toolchain |
---|---|---|
1.9 |
intel/2016b |
|
1.9 |
-PLUMED-2.2.3 |
intel/2016b |
1.10 |
foss/2019b , intel/2019b |
dlb¶
DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., two levels of parallelism) by improving the load balance of the outer level of parallelism (e.g., MPI) by dynamically redistributing the computational resources at the inner level of parallelism (e.g., OpenMP). at run time.
homepage: https://pm.bsc.es/dlb/
version | toolchain |
---|---|
3.2 |
gompi/2022a , iimpi/2022a |
3.3.1 |
gompi/2022a , iimpi/2022a |
dlib¶
Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.
homepage: https://github.com/davisking/dlib
version | versionsuffix | toolchain |
---|---|---|
19.22 |
foss/2021a |
|
19.22 |
-CUDA-11.3.1 |
foss/2021a |
DLPack¶
DLPack is a stable in-memory data structure for an ndarray system to interact with a variety of frameworks.
homepage: https://dmlc.github.io/dlpack/latest/
version | toolchain |
---|---|
0.3 |
GCC/10.3.0 |
dm-reverb¶
Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues.
homepage: https://github.com/deepmind/reverb
version | toolchain |
---|---|
0.2.0 |
foss/2020b |
0.7.0 |
foss/2021b |
dm-tree¶
dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.
homepage: https://github.com/deepmind/tree
version | toolchain |
---|---|
0.1.1 |
GCCcore/8.3.0 |
0.1.5 |
GCCcore/10.2.0 |
0.1.6 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
0.1.8 |
GCCcore/11.3.0 |
DMCfun¶
Diffusion Model of Conflict (DMC) in Reaction Time Tasks
homepage: https://cran.r-project.org/web/packages/DMCfun
version | versionsuffix | toolchain |
---|---|---|
1.3.0 |
-R-3.6.2 |
foss/2019b |
DMLC-Core¶
DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries.
homepage: https://dmlc-core.readthedocs.io/en/latest
version | toolchain |
---|---|
0.5 |
GCC/10.3.0 |
DMTCP¶
DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications.
homepage: http://dmtcp.sourceforge.net/index.html
version | toolchain |
---|---|
2.4.5 |
system |
2.5.0 |
foss/2016a |
2.5.1 |
system |
2.5.2 |
GCCcore/8.3.0 , foss/2016b , foss/2018b |
2.6.0 |
GCCcore/8.2.0 , GCCcore/9.3.0 |
DOLFIN¶
DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations.
homepage: https://bitbucket.org/fenics-project/dolfin
version | versionsuffix | toolchain |
---|---|---|
2018.1.0.post1 |
-Python-3.6.4 |
foss/2018a |
2019.1.0.post0 |
-Python-3.7.4 |
foss/2019b |
dorado¶
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
homepage: https://github.com/nanoporetech/dorado
version | versionsuffix | toolchain |
---|---|---|
0.1.1 |
-CUDA-11.7.0 |
foss/2022a |
Doris¶
Delft object-oriented radar interferometric software
homepage: http://doris.tudelft.nl/
version | toolchain |
---|---|
4.02 |
intel/2017a |
4.04beta4 |
foss/2018a , intel/2017a |
4.06beta2 |
intel/2017a |
DosageConvertor¶
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK. Please note that this tool CANNOT handle missing values in the input files and may NOT work for non-Minimac3/4 VCF files.
homepage: http://genome.sph.umich.edu/wiki/DosageConvertor
version | toolchain |
---|---|
1.0.4 |
GCC/10.2.0 |
dotNET-Core-Runtime¶
.NET is a free, cross-platform, open source developer platform for building many different types of applications.
homepage: https://www.microsoft.com/net/
version | toolchain |
---|---|
2.0.7 |
GCCcore/6.4.0 |
5.0.17 |
GCCcore/10.3.0 |
6.0.1 |
GCCcore/11.2.0 |
dotNET-SDK¶
.NET is a free, cross-platform, open source developer platform for building many different types of applications.
homepage: https://www.microsoft.com/net/
version | versionsuffix | toolchain |
---|---|---|
3.1.300 |
-linux-x64 |
system |
6.0.101 |
-linux-x64 |
system |
double-conversion¶
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
homepage: https://github.com/google/double-conversion
version | toolchain |
---|---|
3.0.3 |
foss/2018a |
3.1.4 |
GCCcore/8.2.0 , GCCcore/8.3.0 |
3.1.5 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/9.3.0 |
3.2.0 |
GCCcore/11.3.0 |
3.2.1 |
GCCcore/12.2.0 |
3.3.0 |
GCCcore/12.3.0 |
DoubletFinder¶
R package for detecting doublets in single-cell RNA sequencing data
homepage: https://github.com/chris-mcginnis-ucsf/DoubletFinder
version | versionsuffix | toolchain |
---|---|---|
2.0.3 |
-R-4.0.0 |
foss/2020a |
2.0.3-20230131 |
-R-4.2.1 |
foss/2022a |
Doxygen¶
Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
homepage: https://www.doxygen.org
version | toolchain |
---|---|
1.8.9.1 |
GCC/4.9.2 |
1.8.10 |
GNU/4.9.3-2.25 , intel/2016.02-GCC-4.9 |
1.8.11 |
GCC/4.9.2 , GCCcore/5.4.0 , foss/2016a , foss/2016b , intel/2016a , intel/2016b , iomkl/2016.07 , iomkl/2016.09-GCC-4.9.3-2.25 |
1.8.13 |
GCCcore/6.3.0 , GCCcore/6.4.0 , gimkl/2017a |
1.8.14 |
GCCcore/6.4.0 , GCCcore/7.2.0 , GCCcore/7.3.0 |
1.8.15 |
GCCcore/8.2.0 |
1.8.16 |
GCCcore/8.3.0 |
1.8.17 |
GCCcore/9.3.0 |
1.8.20 |
GCCcore/10.2.0 |
1.9.1 |
GCCcore/10.3.0 , GCCcore/11.2.0 |
1.9.4 |
GCCcore/11.3.0 |
1.9.5 |
GCCcore/12.2.0 |
1.9.7 |
GCCcore/12.3.0 |
DRAGMAP¶
Dragmap is the Dragen mapper/aligner Open Source Software.
homepage: https://github.com/Illumina/DRAGMAP
version | toolchain |
---|---|
1.3.0 |
foss/2021b |
Drake¶
Drake is a simple-to-use, extensible, text-based data workflow tool that organizes command execution around data and its dependencies.
homepage: https://github.com/Factual/drake
version | versionsuffix | toolchain |
---|---|---|
1.0.3 |
-Java-1.8 |
system |
dRep¶
dRep is a python program which performs rapid pair-wise comparison of genome sets. One of it’s major purposes is for genome de-replication, but it can do a lot more.
homepage: https://drep.readthedocs.io/en/latest/
version | toolchain |
---|---|
3.0.0 |
foss/2021a |
3.4.2 |
foss/2022a |
DROP¶
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
homepage: https://gagneurlab-drop.readthedocs.io
version | versionsuffix | toolchain |
---|---|---|
1.0.3 |
-R-4.0.3 |
foss/2020b |
1.1.0 |
-R-4.0.3 |
foss/2020b |
1.1.1 |
-R-4.1.2 |
foss/2021b |
dropEst¶
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
homepage: https://github.com/hms-dbmi/dropEst
version | versionsuffix | toolchain |
---|---|---|
0.7.1 |
-R-3.4.3 |
intel/2017b |
DSA¶
Digital Sorting Algorithm
homepage: https://github.com/zhandong/DSA
version | versionsuffix | toolchain |
---|---|---|
1.0 |
-R-3.5.1 |
foss/2018b |
dSFMT¶
Double precision SIMD-oriented Fast Mersenne Twister.
homepage: https://github.com/MersenneTwister-Lab/dSFMT
version | toolchain |
---|---|
2.2.5 |
GCCcore/10.2.0 |
DSRC¶
DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.
homepage: http://sun.aei.polsl.pl/dsrc
version | versionsuffix | toolchain |
---|---|---|
2.0rc |
-linux-64-bit |
system |
Dsuite¶
Fast calculation of the ABBA-BABA statistics across many populations/species
homepage: https://github.com/millanek/Dsuite
version | toolchain |
---|---|
20190713 |
iccifort/2019.1.144-GCC-8.2.0-2.31.1 |
20210718 |
GCC/10.3.0 , intel-compilers/2021.2.0 |
dtcmp¶
The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined comparison operations to compare the values of two items which can be arbitrary MPI datatypes. Using these comparison operations, the library provides various routines for manipulating data, which may be distributed over the processes of an MPI communicator.
homepage: https://github.com/LLNL/dtcmp
version | toolchain |
---|---|
1.1.0 |
gompi/2019a , gompi/2020a , iimpi/2019a , iimpi/2020a |
1.1.2 |
gompi/2020b |
dtcwt¶
Dual-Tree Complex Wavelet Transform library for Python
homepage: https://github.com/rjw57/dtcwt
version | versionsuffix | toolchain |
---|---|---|
0.12.0 |
-Python-2.7.15 |
foss/2018b |
0.12.0 |
-Python-3.7.4 |
intel/2019b |
DualSPHysics¶
DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems.
homepage: https://dual.sphysics.org/
version | versionsuffix | toolchain |
---|---|---|
5.0.175 |
GCC/11.2.0 |
|
5.0.175 |
-CUDA-%(cudaver)s |
GCC/11.2.0 |
DUBStepR¶
DUBStepR (Determining the Underlying Basis using Step-wise Regression) is a feature selection algorithm for cell type identification in single-cell RNA-sequencing data.
homepage: https://github.com/prabhakarlab/DUBStepR
version | versionsuffix | toolchain |
---|---|---|
1.2.0 |
-R-4.1.2 |
foss/2021b |
dune-core¶
The Dune core modules build the stable basis of Dune. They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components.
homepage: https://www.dune-project.org/groups/core/
version | toolchain |
---|---|
2.8.0.post1 |
foss/2020b |
dune-fem¶
DUNE-FEM is a discretization module based on DUNE containing all the building blocks required to implement efficient solvers for a wide range of (systems of non linear) partial differential equations. DUNE-FEM can also be used through an extensive Python interface which brings all components of DUNE-FEM and the DUNE core modules to Python.
homepage: https://www.dune-project.org/modules/dune-fem/
version | toolchain |
---|---|
2.8.0.6 |
foss/2020b |
duplex-tools¶
Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for recovering simplex basecalls from incorrectly concatenated pairs.
homepage: https://github.com/nanoporetech/duplex-tools
version | toolchain |
---|---|
0.3.1 |
foss/2022a |
dxpy¶
DNAnexus Platform API bindings for Python
homepage: http://autodoc.dnanexus.com/
version | versionsuffix | toolchain |
---|---|---|
0.266.1 |
-Python-2.7.14 |
intel/2018a |
DyMat¶
Read and process result files from Dymola and OpenModelica with Python.
homepage: https://www.j-raedler.de/projects/DyMat
version | versionsuffix | toolchain |
---|---|---|
0.7 |
-2020-12-12 |
foss/2021b |
E¶
E-ANTIC - ea-utils - earthengine-api - EasyBuild - EasyQC - ecBuild - ecCodes - eccodes-python - ED2 - edlib - EggLib - eggnog-mapper - EGTtools - eht-imaging - Eigen - EigenExa - EIGENSOFT - einops - elastix - elbencho - ELFIO - elfutils - Elk - ELPA - ELPH - elprep - ELSI - ELSI-RCI - Emacs - EMAN2 - EMBOSS - Embree - emcee - EMU - enaBrowserTool - enchant - enchant-2 - EnsEMBLCoreAPI - entrypoints - EPD - EPIC - epiScanpy - eQuilibrator - EricScript - ESL-Bundle - ESM-2 - ESMF - ESMPy - ESMValTool - eSpeak-NG - ESPResSo - Essentia - ETE - ETSF_IO - eudev - Evcxr-REPL - EvidentialGene - evmix - ExaBayes - ExaML - Excel-Writer-XLSX - ExifTool - exiv2 - Exonerate - expat - expect - expecttest - eXpress - Extrae - EZC3D
E-ANTIC¶
E-ANTIC is a C/C++ library to deal with real embedded number fields built on top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as possible exact arithmetic operations and comparisons.
homepage: https://github.com/videlec/e-antic
version | toolchain |
---|---|
0.1.2 |
GCC/8.2.0-2.31.1 |
0.1.5 |
GCC/8.3.0 |
ea-utils¶
Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
homepage: http://expressionanalysis.github.io/ea-utils/
version | toolchain |
---|---|
1.04.807 |
foss/2016a , foss/2016b , intel/2016b |
earthengine-api¶
Python and JavaScript bindings for calling the Earth Engine API
homepage: https://github.com/google/earthengine-api
version | versionsuffix | toolchain |
---|---|---|
0.1.143 |
-Python-2.7.14 |
intel/2018a |
EasyBuild¶
EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
homepage: https://easybuilders.github.io/easybuild
version | toolchain |
---|---|
1.0.0 |
system |
1.0.1 |
system |
1.0.2 |
system |
1.1.0 |
system |
1.2.0 |
system |
1.3.0 |
system |
1.4.0 |
system |
1.5.0 |
system |
1.6.0 |
system |
1.7.0 |
system |
1.8.0 |
system |
1.8.1 |
system |
1.8.2 |
system |
1.9.0 |
system |
1.10.0 |
system |
1.11.0 |
system |
1.11.1 |
system |
1.12.0 |
system |
1.12.1 |
system |
1.13.0 |
system |
1.14.0 |
system |
1.15.0 |
system |
1.15.1 |
system |
1.15.2 |
system |
1.16.0 |
system |
1.16.1 |
system |
1.16.2 |
system |
2.0.0 |
system |
2.1.0 |
system |
2.1.1 |
system |
2.2.0 |
system |
2.3.0 |
system |
2.4.0 |
system |
2.5.0 |
system |
2.6.0 |
system |
2.7.0 |
system |
2.8.0 |
system |
2.8.1 |
system |
2.8.2 |
system |
2.9.0 |
system |
3.0.0 |
system |
3.0.1 |
system |
3.0.2 |
system |
3.1.0 |
system |
3.1.1 |
system |
3.1.2 |
system |
3.2.0 |
system |
3.2.1 |
system |
3.3.0 |
system |
3.3.1 |
system |
3.4.0 |
system |
3.4.1 |
system |
3.5.0 |
system |
3.5.1 |
system |
3.5.2 |
system |
3.5.3 |
system |
3.6.0 |
system |
3.6.1 |
system |
3.6.2 |
system |
3.7.0 |
system |
3.7.1 |
system |
3.8.0 |
system |
3.8.1 |
system |
3.9.0 |
system |
3.9.1 |
system |
3.9.2 |
system |
3.9.3 |
system |
3.9.4 |
system |
4.0.0 |
system |
4.0.1 |
system |
4.1.0 |
system |
4.1.1 |
system |
4.1.2 |
system |
4.2.0 |
system |
4.2.1 |
system |
4.2.2 |
system |
4.3.0 |
system |
4.3.1 |
system |
4.3.2 |
system |
4.3.3 |
system |
4.3.4 |
system |
4.4.0 |
system |
4.4.1 |
system |
4.4.2 |
system |
4.5.0 |
system |
4.5.1 |
system |
4.5.2 |
system |
4.5.3 |
system |
4.5.4 |
system |
4.5.5 |
system |
4.6.0 |
system |
4.6.1 |
system |
4.6.2 |
system |
4.7.0 |
system |
4.7.1 |
system |
EasyQC¶
EasyQC is an R-package that provides advanced functionality to (1) perform file-level QC of single genome-wide association (GWA) data-sets (2) conduct quality control across several GWA data-sets (meta-level QC) (3) simplify data-handling of large-scale GWA data-sets.
version | versionsuffix | toolchain |
---|---|---|
9.2 |
-R-3.3.1 |
intel/2016b |
ecBuild¶
A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems
homepage: https://ecbuild.readthedocs.io/
version | toolchain |
---|---|
3.7.0 |
system |
ecCodes¶
ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).
homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home
version | versionsuffix | toolchain |
---|---|---|
2.7.3 |
intel/2018a |
|
2.7.3 |
-Python-2.7.14 |
intel/2017b |
2.8.2 |
intel/2018a |
|
2.9.2 |
intel/2018b , iomkl/2018b |
|
2.12.5 |
gompi/2019a |
|
2.15.0 |
gompi/2019b , iimpi/2019b |
|
2.17.0 |
foss/2018b , gompi/2019b |
|
2.18.0 |
gompi/2020a |
|
2.20.0 |
gompi/2020b |
|
2.22.1 |
gompi/2021a |
|
2.24.2 |
gompi/2021b , iimpi/2021b |
|
2.27.0 |
gompi/2022a |
eccodes-python¶
Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCodes library.
homepage: https://github.com/ecmwf/eccodes-python
version | versionsuffix | toolchain |
---|---|---|
1.0.0 |
-Python-3.7.4 |
foss/2019b |
1.0.0 |
-Python-3.8.2 |
foss/2020a |
1.1.0 |
foss/2020b |
ED2¶
The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry
homepage: https://github.com/EDmodel/ED2
version | versionsuffix | toolchain |
---|---|---|
20170201 |
intel/2017a |
|
20170201 |
-serial |
intel/2017a |
edlib¶
Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
homepage: https://martinsos.github.io/edlib
version | versionsuffix | toolchain |
---|---|---|
1.3.8.post1 |
-Python-3.7.4 |
GCC/8.3.0 , iccifort/2019.5.281 |
1.3.8.post1 |
-Python-3.8.2 |
GCC/9.3.0 |
1.3.8.post2 |
-Python-3.8.2 |
iccifort/2020.1.217 |
1.3.9 |
GCC/10.2.0 , GCC/10.3.0 , GCC/11.2.0 , GCC/11.3.0 |
EggLib¶
EggLib is a C++/Python library and program package for evolutionary genetics and genomics.
homepage: http://egglib.sourceforge.net/
version | toolchain |
---|---|
2.1.10 |
intel/2016a |
eggnog-mapper¶
EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
homepage: https://github.com/eggnogdb/eggnog-mapper
version | versionsuffix | toolchain |
---|---|---|
1.0.3 |
-Python-2.7.14 |
intel/2018a |
2.1.4 |
foss/2020b |
|
2.1.7 |
foss/2021b |
|
2.1.10 |
foss/2020b |
EGTtools¶
EGTtools provides a centralized repository with analytical and numerical methods to study/model game theoretical problems under the Evolutionary Game Theory (EGT) framework.
homepage: https://github.com/Socrats/EGTTools
version | toolchain |
---|---|
0.1.10.dev2 |
foss/2021b |
0.1.11 |
foss/2022a |
eht-imaging¶
Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods.
homepage: https://github.com/achael/eht-imaging
version | toolchain |
---|---|
1.2.2 |
foss/2021a |
Eigen¶
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
homepage: https://eigen.tuxfamily.org
version | toolchain |
---|---|
3.2.3 |
foss/2016a , foss/2016b |
3.2.5 |
system |
3.2.6 |
system |
3.2.7 |
foss/2016a , intel/2016a |
3.2.8 |
foss/2016a , intel/2016a , system |
3.2.9 |
foss/2016b , intel/2016b |
3.2.10 |
intel/2016b |
3.3.2 |
foss/2016b , intel/2016b |
3.3.3 |
GCCcore/6.3.0 , intel/2016b |
3.3.4 |
system |
3.3.5 |
system |
3.3.7 |
GCCcore/9.3.0 , system |
3.3.8 |
GCCcore/10.2.0 |
3.3.9 |
GCCcore/10.2.0 , GCCcore/10.3.0 , GCCcore/11.2.0 |
3.4.0 |
GCCcore/10.2.0 , GCCcore/11.2.0 , GCCcore/11.3.0 , GCCcore/12.2.0 , GCCcore/12.3.0 |
EigenExa¶
EigenExa, a part of KMATHLIB, is a high performance eigen-solver.
homepage: https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/
version | toolchain |
---|---|
2.11 |
intel/2020b |
EIGENSOFT¶
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
homepage: http://www.hsph.harvard.edu/alkes-price/software/
version | toolchain |
---|---|
6.0.1 |
foss/2016a |
6.1.1 |
foss/2016a |
6.1.4 |
foss/2016b |
7.2.1 |
foss/2018b , foss/2019a , foss/2019b , foss/2021a , intel/2019a |
einops¶
Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.
homepage: https://einops.rocks/
version | toolchain |
---|---|
0.3.2 |
GCCcore/10.2.0 |
0.4.1 |
GCCcore/10.3.0 , GCCcore/11.3.0 |
elastix¶
elastix: a toolbox for rigid and nonrigid registration of images.
homepage: http://elastix.isi.uu.nl/
version | toolchain |
---|---|
4.9.0 |
foss/2018a |
elbencho¶
A distributed storage benchmark for files, objects & blocks with support for GPUs
homepage: https://github.com/breuner/elbencho
version | toolchain |
---|---|
2.0-3 |
GCC/10.3.0 |
ELFIO¶
ELFIO is a header-only C++ library intended for reading and generating files in the ELF binary format.
homepage: http://elfio.sourceforge.net
version | toolchain |
---|---|
3.9 |
system |
elfutils¶
The elfutils project provides libraries and tools for ELF files and DWARF data.
homepage: https://elfutils.org/
version | toolchain |
---|---|
0.182 |
GCCcore/9.3.0 |
0.183 |
GCCcore/10.2.0 |
0.185 |
GCCcore/10.3.0 , GCCcore/11.2.0 , GCCcore/8.2.0 , GCCcore/8.3.0 |
0.187 |
GCCcore/11.3.0 |
0.189 |
GCCcore/12.2.0 , GCCcore/12.3.0 |
Elk¶
An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably.
homepage: http://elk.sourceforge.net/
version | toolchain |
---|---|
4.0.15 |
intel/2016b |
4.3.6 |
intel/2017a |
6.3.2 |
intel/2019b |
7.0.12 |
foss/2020b |
7.2.42 |
foss/2021a |
8.5.2 |
foss/2022a |
ELPA¶
Eigenvalue SoLvers for Petaflop-Applications.
homepage: https://elpa.mpcdf.mpg.de/
version | versionsuffix | toolchain |
---|---|---|
2015.02.002 |
foss/2018a , gimkl/2017a , intel/2018a |
|
2016.05.004 |
intel/2016b , intel/2017a |
|
2016.11.001.pre |
foss/2018b , intel/2018b |
|
2017.11.001 |
foss/2018b , intel/2018a , intel/2018b |
|
2018.05.001 |
foss/2018b , intel/2018b |
|
2018.11.001 |
intel/2019a |
|
2019.11.001 |
foss/2019b , foss/2020a , intel/2019b , intel/2020a , iomkl/2019b |
|
2020.05.001 |
intel/2020a |
|
2020.11.001 |
foss/2020b , intel/2020b |
|
2021.05.001 |
foss/2021a , foss/2021b , intel/2021a , intel/2021b |
|
2021.05.002 |
intel/2020b |
|
2021.11.001 |
foss/2021b , foss/2022a , intel/2021b , intel/2022a |
|
2022.05.001 |
foss/2022a , foss/2022b , intel/2022a , intel/2022b |
|
2022.05.001 |
-CUDA-11.7.0 |
foss/2022a |
2022.05.001 |
-CUDA-12.0.0 |
foss/2022b |
ELPH¶
ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).
homepage: http://ccb.jhu.edu/software/ELPH/index.shtml
version | toolchain |
---|---|
1.0.1 |
foss/2018b |
elprep¶
elPrep is a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.
homepage: https://github.com/ExaScience/elprep
version | toolchain |
---|---|
5.1.1 |
system |
ELSI¶
ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
homepage: https://wordpress.elsi-interchange.org/
version | versionsuffix | toolchain |
---|---|---|
2.5.0 |
foss/2019b , intel/2019b |
|
2.5.0 |
-PEXSI |
foss/2019b , intel/2019b |
2.6.4 |
-PEXSI |
foss/2020b , intel/2020b |
2.7.1 |
-PEXSI |
foss/2021a , intel/2021a |
ELSI-RCI¶
ELSI-RCI provides and enhances open-source software packages which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory.
homepage: https://wordpress.elsi-interchange.org/
version | toolchain |
---|---|
0.1.0 |
GCC/10.3.0 , GCC/11.2.0 , foss/2020b , intel-compilers/2021.2.0 , intel-compilers/2021.4.0 , intel/2020b |
Emacs¶
GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
homepage: https://www.gnu.org/software/emacs/
version | versionsuffix | toolchain |
---|---|---|
24.3 |
GCC/4.8.3 |
|
24.3 |
-bare |
GCC/4.8.3 |
24.4 |
GCC/4.9.2 |
|
24.5 |
GCC/4.9.3-2.25 |
|
25.1 |
foss/2016a |
|
25.3 |
GCCcore/6.3.0 , GCCcore/6.4.0 , GCCcore/7.3.0 |
|
26.3 |
GCCcore/8.3.0 |
|
27.1 |
GCCcore/10.2.0 , GCCcore/9.3.0 |
|
27.2 |
GCCcore/11.2.0 |
|
28.1 |
GCCcore/10.2.0 |
EMAN2¶
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
homepage: https://blake.bcm.edu/emanwiki/EMAN2
version | versionsuffix | toolchain |
---|---|---|
2.3 |
system |
|
2.3 |
-Python-2.7.15 |
foss/2019a , fosscuda/2019a |
2.21a |
-Python-2.7.14-Boost-1.63.0 |
foss/2018a |
EMBOSS¶
EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
homepage: http://emboss.sourceforge.net/
version | versionsuffix | toolchain |
---|---|---|
6.6.0 |
GCC/8.2.0-2.31.1 , foss/2016b , foss/2018b , foss/2021a , foss/2021b , iccifort/2019.1.144-GCC-8.2.0-2.31.1 , intel/2017a , intel/2018b |
|
6.6.0 |
-Java-11 |
GCC/8.3.0 |
6.6.0 |
-Java-13 |
GCC/10.2.0 |
6.6.0 |
-X11-20170314 |
intel/2017a |
Embree¶
Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.
homepage: https://embree.github.io/
version | toolchain |
---|---|
3.4.0 |
iccifort/2018.1.163-GCC-6.4.0-2.28 |
3.13.4 |
system |
emcee¶
Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet!
homepage: https://dfm.io/emcee
version | versionsuffix | toolchain |
---|---|---|
2.2.1 |
foss/2019a |
|
2.2.1 |
-Python-2.7.15 |
foss/2018b , intel/2018b |
2.2.1 |
-Python-3.6.6 |
foss/2018b , intel/2018b |
EMU¶
EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets
homepage: http://www.popgen.dk/software/index.php/EMU
version | versionsuffix | toolchain |
---|---|---|
0.66 |
-Python-3.7.4 |
foss/2019b |
enaBrowserTool¶
enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required.
homepage: https://github.com/enasequence/enaBrowserTools/
version | versionsuffix | toolchain |
---|---|---|
1.5.4 |
-Python-3.7.2 |
GCCcore/8.2.0 |
1.6 |
GCCcore/10.3.0 |
enchant¶
Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.
homepage: https://abiword.github.io/enchant/
version | toolchain |
---|---|
1.6.1 |
intel/2017a |
enchant-2¶
Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant.
homepage: https://github.com/AbiWord/enchant
version | toolchain |
---|---|
2.3.3 |
GCCcore/11.2.0 , GCCcore/11.3.0 |
EnsEMBLCoreAPI¶
The Ensembl Core Perl API and SQL schema
homepage: https://www.ensembl.org/info/docs/api/index.html
version | versionsuffix | toolchain |
---|---|---|
96.0-r20190601 |
-Perl-5.28.1 |
foss/2019a |
entrypoints¶
Entry points are a way for Python packages to advertise objects with some common interface.
homepage: https://github.com/takluyver/entrypoints
version | versionsuffix | toolchain |
---|---|---|
0.2.2 |
-Python-2.7.11 |
foss/2016a |
0.2.2 |
-Python-2.7.12 |
foss/2016b , intel/2016b |
0.2.2 |
-Python-3.5.1 |
foss/2016a |
0.2.2 |
-Python-3.5.2 |
intel/2016b |
EPD¶
The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.
homepage: http://www.enthought.com/products/edudownload.php
version | toolchain |
---|---|
7.3-2-rh5 |
system |
EPIC¶
Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data.
homepage: https://gfellerlab.shinyapps.io/EPIC_1-1
version | versionsuffix | toolchain |
---|---|---|
1.1 |
-R-3.5.1 |
foss/2018b |
epiScanpy¶
EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018) [Wolf18].
homepage: https://github.com/colomemaria/episcanpy
version | toolchain |
---|---|
0.3.1 |
foss/2021a |