ADMIXTURE/1.3.0-x86_64
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.
AGAT/0.9.2-GCC-11.2.0
AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format.
ASE/3.22.0-foss-2020b
ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.
ATK/2.38.0-GCCcore-11.3.0
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.
Abseil/20240722.0-GCCcore-13.3.0
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.
AlphaPulldown/2.0.3-foss-2023a-CUDA-12.1.1
AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer
Apptainer/1.1.6
Apptainer is a portable application stack packaging and runtime utility.
Armadillo/14.0.3-foss-2024a
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.
ArrayFire/3.8.1-foss-2019b-CUDA-10.2.89
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.
Arriba/2.4.0-GCC-12.2.0
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.
Arrow/17.0.0-gfbf-2024a
Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data.
Aspera-CLI/3.9.6.1467.159c5b1
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.
Aspera-Connect/3.9.6
Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.
Autoconf/2.72-GCCcore-13.3.0
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.
Automake/1.16.5
Automake: GNU Standards-compliant Makefile generator
BCFtools/1.19-GCC-13.2.0
Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools
BEAST/10.5.0-beta3-GCC-12.3.0-CUDA-12.1.1
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. 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.
BEDOPS/2.4.41-foss-2021b
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.
BEDTools/2.31.0-GCC-12.3.0
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.
BGEN/1.1.7
This repository contains a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software, or as a reference for developers writing their own implementations of the BGEN format. Please cite: Band, G. and Marchini, J., “BGEN: a binary file format for imputed genotype and haplotype data”, bioArxiv 308296; doi: https://doi.org/10.1101/308296
BGEN-enkre/1.1.7-GCC-11.2.0
This repository contains a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software, or as a reference for developers writing their own implementations of the BGEN format. Please cite: Band, G. and Marchini, J., “BGEN: a binary file format for imputed genotype and haplotype data”, bioArxiv 308296; doi: https://doi.org/10.1101/308296
BLAST+/2.16.0-gompi-2024a
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.
BLAT/3.5-GCC-8.3.0
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
BLIS/1.0-GCC-13.3.0
BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
BPCells/0.3.0-foss-2024a
Single-cell transcriptome sequencing (sc-RNA-seq) experiments allow us to discover new cell types and help us understand how they arise in development. The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
BUStools/0.40.0-foss-2019b
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.
BWA/0.7.18-GCCcore-13.3.0
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
BamTools/2.5.2-GCC-13.3.0
BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.
BaseSpaceCLI/1.5.1
BaseSpace is a powerful website where biologists and informaticians can easily store, analyze, and share genetic data. BaseSpace is a commerical product from Illumina.
Bazel/7.1.1-GCCcore-13.2.0
Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google’s software.
Beagle/5.2.1
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
Beast/10.5.0-beta3-GCC-12.3.0-beagle-lib-4.0.1-CUDA-12.1.1
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. 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.
Beast2/2.7.7-GCC-12.3.0-beagle-lib-4.0.1-CUDA-12.1.1
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.
Bio-SearchIO-hmmer/1.7.3-GCC-10.2.0
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.
BioPerl/1.7.8-GCCcore-10.2.0
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.
Biopython/1.84-foss-2024a
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.
Bismark/0.24.1-GCC-12.2.0
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Bison/3.8.2-GCCcore-13.2.0
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.
Boost.Python/1.64.0-gompi-2019b
Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
Bowtie/1.3.0-GCC-10.2.0
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
Bowtie2/2.5.4-GCC-13.2.0
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.
Brotli/1.1.0-GCCcore-13.2.0
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.
CD-HIT/4.8.1-foss-2019b
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
CFITSIO/4.4.1-GCCcore-13.3.0
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
CMake/3.29.3-GCCcore-13.3.0
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CNVkit/0.9.9-foss-2021b-R-4.2.0
A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
CRISPResso2/2.3.1-foss-2023b
CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments.
CRIU/3.13-foss-2019b-Python-3.7.4
Checkpoint/Restore In Userspace (CRIU) is a Linux software which can freeze a running container (or an individual application) and checkpoint its state to disk. The data saved can be used to restore the application and run it exactly as it was during the time of the freeze. Using this functionality, application or container live migration, snapshots, remote debugging, and many other things are now possible.
CUDA/12.6.0
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.
CUDAcore/11.1.1-GCCcore-10.2.0
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.
CUTLASS/3.4.0-foss-2023a-CUDA-12.1.1
CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-matrix multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these “moving parts” into reusable, modular software components abstracted by C++ template classes. Primitives for different levels of a conceptual parallelization hierarchy can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications.
Cbc/2.10.5-foss-2022b
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.
CellBender/0.2.2-foss-2021b-CUDA-11.4.1
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
CellProfiler/4.2.7-foss-2023a
CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
CellRanger/10.0.0
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.
CellRanger-ARC/2.1.0
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.
CellRanger-ATAC/2.0.0
Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
CellRank/2.0.2-foss-2023a
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.
Cellpose/0.6.5-fosscuda-2020b
Cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu.
Cereal/1.3.2-GCCcore-12.2.0
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
Cgl/0.60.8-foss-2023b
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.
Check/0.15.2-GCCcore-10.2.0
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.
Clair3/1.0.4-foss-2022a
Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.
Clang/18.1.8-GCCcore-13.3.0
C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library – use libstdc++ from GCC.
Clp/1.17.9-foss-2023b
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.
Clustal-Omega/1.2.4-GCC-8.3.0
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
ClustalW2/2.1-foss-2019b
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
Cluster-Buster/0.0-GCC-12.2.0
Cluster-Buster is a program for finding interesting functional regions, such as transcriptional enhancers, in DNA sequences.
Cogent_NGS_Immune_Profiler/v2.0-foss-2024a
Cogent NGS Immune Profiler (CogentIP) is software designed to analyze sequence data stored in FASTQ files generated by Illumina sequencers from libraries prepared using certain Takara Bio immune profiling kits.
Coin/4.0.0-GCC-11.2.0
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.
CoinUtils/2.11.10-GCC-13.2.0
CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.
Control-FREEC/11.5-GCC-8.3.0
Copy number and genotype annotation from whole genome and whole exome sequencing data.
Coreutils/8.32-GCCcore-8.3.0
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.
CrossMap/0.7.3-foss-2023b
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.
Cython/3.0.10-GCCcore-13.2.0
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
DB/18.1.40-GCCcore-11.3.0
Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
DBus/1.15.8-GCCcore-13.2.0
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.
DLPack/0.8-GCC-11.3.0
DLPack is a stable in-memory data structure for an ndarray system to interact with a variety of frameworks.
DMLC-Core/0.5-GCC-11.3.0
DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries.
DeepCell/0.11.1-foss-2021b-CUDA-11.4.1
deepcell-tf is a deep learning library for single-cell analysis of biological images.This library allows users to apply pre-existing models to imaging data as well as to develop new deep learning models for single-cell analysis.
DeepTCR/2.1.27-foss-2021b-CUDA-11.4.1
DeepTCR is a python package that has a collection of unsupervised and supervised deep learning methods to parse TCRSeq data.
Delly/0.9.1-gompi-2020b
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.
DeltaLake/0.15.1-gfbf-2023a
Native Delta Lake Python binding based on delta-rs with Pandas integration. The Delta Lake project aims to unlock the power of the Deltalake for as many users and projects as possible by providing native low-level APIs aimed at developers and integrators, as well as a high-level operations API that lets you query, inspect, and operate your Delta Lake with ease.
DendroPy/5.0.1-GCCcore-13.2.0
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
Deprecated/1.2.18-gfbf-2024a
If you need to mark a function or a method as deprecated, you can use the @deprecated decorator.
DiMSum/1.2.9-foss-2021b-R-4.2.0
An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies.
Doxygen/1.11.0-GCCcore-13.3.0
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.
EIGENSOFT/7.2.1-foss-2019b
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.
EMAN2/2.3-foss-2019b-Python-2.7.16
EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
EMBOSS/6.6.0-foss-2023b
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.
EPACTS/3.3.2-foss-2020b
EPACTS is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers.
ESS/18.10.2
Emacs Speaks Statistics (ESS) is an add-on package for emacs text editors such as GNU Emacs and XEmacs. It is designed to support editing of scripts and interaction with various statistical analysis programs such as R, S-Plus, SAS, Stata and OpenBUGS/JAGS.
EasyBuild/5.2.1
EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
Eigen/3.4.0-GCCcore-11.3.0
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
Emacs/27.1-GCCcore-10.2.0
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.
Enrich2/1.3.1-foss-2020b-Python-2.7.18
Enrich2 is a general software tool for processing, analyzing, and visualizing data from deep mutational scanning experiments.
Enrich2/1.3.1-foss-2020b-Python-2.7.18
Enrich2 is a general software tool for processing, analyzing, and visualizing data from deep mutational scanning experiments.
FASTX-Toolkit/0.0.14-GCCcore-8.3.0
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
FFTW/3.3.10-GCC-11.3.0
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
FFTW.MPI/3.3.10-gompi-2023b
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
FFmpeg/6.0-GCCcore-12.3.0
A complete, cross-platform solution to record, convert and stream audio and video.
FLAC/1.4.3-GCCcore-13.3.0
FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.
FLAIR/2.0-foss-2023a
FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
FLASH/2.2.00-GCCcore-13.2.0
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
FLTK/1.3.5-GCC-8.3.0
FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
FTGL/2.3-GCCcore-10.2.0
FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications.
FastQC/0.12.1-Java-11
FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
FastTree/2.1.11-GCCcore-11.3.0
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
Fiji/2.9.0-Java-1.8
Fiji is an image processing package—a ‘batteries-included’ distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1
FlashPCA2/2.0-GCC-10.2.0
FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data.
Flask/2.3.3-GCCcore-12.3.0
Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors
Flax/0.8.4-gfbf-2023a-CUDA-12.1.1
Flax is a high-performance neural network library and ecosystem for JAX that is designed for flexibility: Try new forms of training by forking an example and by modifying the training loop, not by adding features to a framework.
FlexiBLAS/3.4.4-GCC-13.3.0
FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
FreeImage/3.18.0-GCCcore-11.2.0
FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today’s multimedia applications. FreeImage is easy to use, fast, multithreading safe.
FreeTDS/1.3.6-GCCcore-11.2.0
FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases.
GATK/4.4.0.0-GCCcore-12.2.0-Java-17
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
GCC/13.3.0
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,…).
GCCcore/13.3.0
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,…).
GCTA/1.92.2beta
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.
GConf/3.2.6-GCCcore-10.2.0
GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage.
GDAL/3.10.0-foss-2024a
GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
GISTIC/2.0.23-GCCcore-8.3.0
GISTIC is a tool to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, GISTIC estimates the background rates for each category as well as defines the boundaries of SCNA regions.
GLFW/3.4-GCCcore-12.2.0
GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop
GLIPH2/0.1
GLIPH 2 clusters TCRs that are predicted to bind the same MHC-restricted peptide antigen.
GLPK/5.0-GCCcore-12.3.0
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
GMP/6.3.0-GCCcore-13.2.0
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
GMime/3.2.7-GCCcore-8.3.0
The GMime package contains a set of utilities for parsing and creating messages using the Multipurpose Internet Mail Extension (MIME) as defined by the applicable RFCs.
GObject-Introspection/1.80.1-GCCcore-13.3.0
GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
GRIDSS/2.13.2-foss-2021b
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
GROMACS/2024.4-foss-2023b
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI binaries for both single and double precision. It also contains the gmxapi extension for the single precision MPI build.
GSEA/4.3.2
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
GSL/2.8-GCC-13.3.0
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
GST-plugins-bad/1.22.5-GCC-12.3.0
GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
GST-plugins-base/1.22.5-GCC-12.3.0
GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
GStreamer/1.22.5-GCC-12.3.0
GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
GTK+/3.24.23-GCCcore-10.2.0
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
GTK2/2.24.33-GCCcore-11.3.0
The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
GTK3/3.24.39-GCCcore-13.2.0
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
GTK4/4.13.1-GCC-12.3.0
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
GTS/0.7.6-GCCcore-11.2.0
GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
Garnett/20220903-foss-2021b-R-4.2.2
Garnett is a software package that faciliates automated cell type classification from single-cell expression data.
Gdk-Pixbuf/2.42.10-GCCcore-12.3.0
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
Geekbench/5.4.1
Geekbench 5 is a cross-platform benchmark that measures your system’s performance with the press of a button.
GenomeSTRiP/2.00.1958-GCCcore-8.3.0-Java-11
Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovery and genotyping of structural variation using whole-genome sequencing data. The methods used in Genome STRiP are designed to find shared variation using data from multiple individuals. Genome STRiP looks both across and within a set of sequenced genomes to detect variation.
Ghostscript/10.03.1-GCCcore-13.3.0
Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
Giotto/1.0.0-foss-2019b-R-4.0.2
The Giotto package consists of two modules, Giotto Analyzer and Viewer, which provide tools to process, analyze and visualize single-cell spatial expression data.
Globus-CLI/3.29.0-GCCcore-12.2.0
A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.
GlobusConnectPersonal/3.2.0-GCCcore-11.2.0
Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computer or laptop—even if it’s behind a firewall and you don’t have administrator privileges.
GnuTLS/3.8.4-GCCcore-12.3.0
GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.
Go/1.25.5
Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
GoPeaks/1.0.0
GoPeaks is a peak caller designed for CUT&TAG/CUT&RUN sequencing data.
Gradle/8.6-Java-17
Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster.
Graphviz/10.0.1-GCCcore-13.2.0
Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
Greenlet/2.0.2-GCCcore-12.3.0
The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called “tasklets”. Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on “channels”. A “greenlet”, on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.
Guile/3.0.9-GCCcore-12.3.0
Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts.
Gurobi/11.0.2
The Gurobi Optimizer allows users to state their toughest business problems as mathematical models, and then automatically considers billions or even trillions of possible solutions to find the best one. Our solver can be used as both a decision-making assistant, to help guide the choices of a skilled expert, or as a fully automated tool to make decisions with no human intervention.
HDF/4.3.0-GCCcore-13.3.0
HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
HDF5/1.14.5-gompi-2024a
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
HH-suite/3.3.0-gompi-2022a
The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
HISAT2/2.2.1-gompi-2021b
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
HLA-HD/1.6.1-GCC-11.2.0
HLA-HD (HLA typing from High-quality Dictionary) can accurately determine HLA alleles with 6-digit precision from NGS data (fastq format). RNA-Seq data can also be applied.
HMMER/3.4-gompi-2023a
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
HOME/1.0.0-foss-2019b-Python-3.7.4
HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification. The method uses histogram of methylation features and the linear Support Vector Machine (SVM) to identify DMRs from whole genome bisulfite sequencing (WGBS) data.
HOMER/5.1-foss-2023a-R-4.3.2
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
HTSeq/0.11.3-foss-2020b
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
HTSlib/1.21-GCC-13.3.0
A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
Hail/0.2.64-foss-2020b
Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data.
HiC-Pro/3.1.0-foss-2021b
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps.
Highway/1.0.7-GCCcore-13.2.0
Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to ‘lanes’.
Homer/4.11-Perl-5.30.0
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.
HyPhy/2.5.60-gompi-2022a
HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning
Hypre/2.25.0-foss-2022a
Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
ICU/75.1-GCCcore-13.3.0
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
IGV/2.15.4-Java-11
This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.
IGVTools/2.4.16-Java-1.8
This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.
IPython/8.28.0-GCCcore-13.3.0
IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
IRIS/2.0.1
IRIS Isoform peptides from RNA splicing for Immunotherapy target Screening
IRkernel/1.3.2-gfbf-2023b-R-4.4.0
The R kernel for the ‘Jupyter’ environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network.
Imath/3.1.11-GCCcore-13.3.0
Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
Infernal/1.1.4-foss-2021b
Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities.
JAGS/4.3.2-foss-2023b
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
Jansson/2.14-GCC-12.3.0
Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite
JasPer/4.2.4-GCCcore-13.3.0
The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
Java/21.0.2
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
JsonCpp/1.9.5-GCCcore-12.2.0
JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
Julia/1.12.2
Julia is a high-level, high-performance dynamic programming language for numerical computing
JupyterHub/4.0.1-GCCcore-12.2.0
JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.
JupyterLab/4.2.5-GCCcore-13.3.0
JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.
JupyterNotebook/7.0.2-GCCcore-12.3.0
The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.
Keras/2.4.3-foss-2020b
Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow.
Kraken2/2.1.3-gompi-2022b
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
Krona/2.7.1-GCCcore-9.3.0-Perl-5.30.2
Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats.
LAME/3.100-GCCcore-12.2.0
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
LAPACK/3.12.0-GCC-11.2.0
LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
LEMON/1.3.1-GCC-13.2.0
LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks.
LERC/4.0.0-GCCcore-13.2.0
LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds).
LIBSVM/3.25-GCCcore-10.2.0
LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.
LLVM/18.1.8-GCCcore-13.3.0-minimal
The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation (“LLVM IR”). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
LMDB/0.9.31-GCCcore-13.2.0
LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
Leptonica/1.83.0-GCCcore-11.2.0
Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
LibSoup/3.5.1-GCC-12.3.0
libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications.
LittleCMS/2.16-GCCcore-13.3.0
Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
LoomXpy/0.4.2-foss-2022b
Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons
Lua/5.4.6-GCCcore-12.3.0
Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
M4/1.4.19-GCCcore-11.2.0
GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
MACHINA/1.2-GCC-13.2.0
MACHINA is a computational framework for inferring migration patterns between a primary tumor and metastases using DNA sequencing data.
MAESTRO/1.2.1-foss-2019b-Python-3.7.4
MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. MAESTRO combines several dozen tools and packages to create an integrative pipeline, which enables scRNA-seq and scATAC-seq analysis from raw sequencing data (fastq files) all the way through alignment, quality control, cell filtering, normalization, unsupervised clustering, differential expression and peak calling, celltype annotation and transcription regulation analysis.
MAFFT/7.526-GCC-13.2.0-with-extensions
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
MAGeCK/0.5.9.5-gfbf-2022b
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu’s lab at Dana-Farber Cancer Institute, and is being actively updated by Wei Li lab from Children’s National Medical Center.
MAGeCK-VISPR/0.5.5-Python-3.7.4
MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens The workflow combines the MAGeCK algorithm to identify essential genes from CRISPR/Cas9 screens considering multiple conditions with VISPR to interactively explore results and quality control in a web-based frontend.
MEGAHIT/1.2.9-GCCcore-13.3.0
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
MEGAN/6.25.3-Java-17
MEGAN is a comprehensive toolbox for interactively analyzing microbiome data
MEME/5.5.1-gompi-2021b
The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
METIS/5.1.0-foss-2020b
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
MLflow/2.10.2-gfbf-2023a
MLflow is a platform to streamline machine learning development, including tracking experiments, packaging code into reproducible runs, and sharing and deploying models.
MPC/1.3.1-GCCcore-12.3.0
Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.
MPFR/4.2.1-GCCcore-13.2.0
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MUMmer/4.0.0rc1-GCCcore-12.3.0
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
MUSCLE/5.1.0-GCCcore-12.3.0
MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.
Magic-BLAST/1.5.0-Linux_x86_64
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
Mako/1.3.5-GCCcore-13.3.0
A super-fast templating language that borrows the best ideas from the existing templating languages
MariaDB/11.7.0-GCC-13.3.0
MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.
Markdown/3.7-GCCcore-13.3.0
This is a Python implementation of John Gruber’s Markdown. It is almost completely compliant with the reference implementation, though there are a few known issues. Additional features are supported by the Available Extensions.
MathWorksServiceHost/2024.13.0.2
MathWorks Service Host is a collection of background processes that provide required services to MATLAB and other MathWorks products. Starting from MATLAB Release 2024a, MATLAB requires MathWorks Service Host.
Maven/3.6.3
Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project’s build, reporting and documentation from a central piece of information.
MaxQuant/2.7.3.0
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.
Mesa/24.1.3-GCCcore-13.3.0
Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
Meson/1.4.0-GCCcore-13.3.0
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
Miniforge3/24.1.2-0
Miniforge is a free minimal installer for conda and Mamba specific to conda-forge.
Mono/6.12.0.199-GCCcore-12.2.0
An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
Monocle3/1.3.1-foss-2021b-R-4.2.2
Single-cell transcriptome sequencing (sc-RNA-seq) experiments allow us to discover new cell types and help us understand how they arise in development. The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
MoreRONN/4.9-foss-2019b
MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography.
MotionCor2/1.4.2-gcccuda-2020b
MotionCor2 correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960
MuSE/2.0.1-GCC-11.2.0
An accurate and ultra-fast somatic mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples.
MultiQC/1.21-foss-2023a
Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools.
MutSig/2
MutSig stands for “Mutation Significance”. MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
MutSig2CV/3.11
MutSig2CV analyzes somatic point mutations discovered in DNA sequencing, identifying genes mutated more often than expected by chance given inferred background mutation processes.
MutSigCV/1.4.1
MutSigCV accepts whole genome or whole exome sequencing data from multiple samples, with information about point mutations, small insertions/deletions, and coverage, and identifies genes that are mutated more often than one would expect by chance.
NAMD/2.14-foss-2020a-mpi
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NCCL/2.22.3-GCCcore-13.3.0-CUDA-12.6.0
The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
NGS/2.11.2-GCCcore-11.2.0
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
NLTK/3.8.1-foss-2023a
NLTK is a leading platform for building Python programs to work with human language data.
NLopt/2.7.1-GCCcore-13.3.0
NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.
NSPR/4.35-GCCcore-12.2.0
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
NSS/3.94-GCCcore-13.2.0
Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
NextGenMap/0.5.5-GCC-11.2.0
NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime.
OpenCV/4.5.5-foss-2021b-contrib
OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository.
OpenEXR/3.2.4-GCCcore-13.3.0
OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications
OpenJPEG/2.5.2-GCCcore-13.3.0
OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.
OpenPGM/5.2.122-GCCcore-9.3.0
OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.
OpenSSL/3
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.
OptiType/1.3.5-foss-2019b-Python-2.7.16
OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.
Osi/0.108.9-GCC-13.2.0
Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming.
PCRE/8.45-GCCcore-11.3.0
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PCRE2/10.43-GCCcore-13.3.0
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PDBFixer/1.7-foss-2020b
PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them.
PDFCrop/0.4b
PDFCrop is a Perl script that crops the white margins of PDF pages and rescales them to fit a standard size sheet of paper. It makes the printed pages far more attractive to read!
PDM/2.18.2-GCCcore-13.3.0
A modern Python package and dependency manager supporting the latest PEP standards.
PEAR/0.9.11-GCC-11.3.0
PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
PETSc/3.17.4-foss-2022a
PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
PHASE/2.1.2-GCCcore-8.3.0
PHASE is a program implementing the method for reconstructing haplotypes from population data
PLINK2/20210826-linux_x86_64
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data.
PLUMED/2.7.2-foss-2020b
PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
PMIx/5.0.2-GCCcore-13.3.0
Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions
PROJ/9.6.2-GCCcore-12.3.0
Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
Pandoc/2.13
If you need to convert files from one markup format into another, pandoc is your swiss-army knife
Pango/1.54.0-GCCcore-13.3.0
Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
ParMETIS/4.0.3-gompi-2022a
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
Parallel-Hashmap/1.36-GCCcore-11.3.0
Parallel Hashmap is built on a modified version of Abseil’s flat_hash_map. Parallel Hashmap has lower space requirements, is nearly as fast as the underlying flat_hash_map, and can be used from multiple threads with high levels of concurrency.
Parallel-Hashmap/1.36-GCCcore-11.3.0
Parallel Hashmap is built on a modified version of Abseil’s flat_hash_map. Parallel Hashmap has lower space requirements, is nearly as fast as the underlying flat_hash_map, and can be used from multiple threads with high levels of concurrency.
Parsl/2024.4.22-GCCcore-13.2.0
Parsl extends parallelism in Python beyond a single computer. You can use Parsl just like Python’s parallel executors but across multiple cores and nodes. However, the real power of Parsl is in expressing multi-step workflows of functions. Parsl lets you chain functions together and will launch each function as inputs and computing resources are available.
Perl/5.38.2-GCCcore-13.3.0
Larry Wall’s Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality.
PhyML/3.3.20220408-foss-2023a
PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework.
Pillow/10.4.0-GCCcore-13.3.0
Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
Pillow-SIMD/10.4.0-GCCcore-13.3.0
Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
Porechop/0.2.4-GCCcore-12.3.0
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity
PostgreSQL/16.4-GCCcore-13.3.0
PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
ProteinMPNN/1.0.1-20230627-foss-2022a-CUDA-11.7.0
A deep learning based protein sequence design method is described that is widely applicable to current design challenges and shows outstanding performance in both in silico and experimental tests.
PuLP/2.7.0-foss-2022b
PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems.
PyClone/2020.9b2-GCCcore-10.2.0
PyClone is a Python package that wraps rclone and provides a threaded interface for an installation at the host or container level.
PyGEOS/0.14-gfbf-2023a
PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance improvement when operating on arrays of geometries.
PyGObject/3.46.0-GCCcore-12.3.0
PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.
PyPy/7.3.18
A fast, compliant alternative implementation of Python
PyQt5/5.15.1-GCCcore-10.2.0
PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.
PyRosetta/4.387-gompi-2023a
PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
PySide6/6.5.0-GCCcore-12.2.0
PySide6 is the official Python module from the Qt for Python project, which provides access to the complete Qt 6.5+ framework.
PyStan/3.5.0-foss-2021b
Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.
PyTables/3.9.2-foss-2023a
PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases.
PyTorch/2.1.2-foss-2023a-CUDA-12.1.1
Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first.
PyVCF3/1.0.3-GCCcore-11.3.0
A VCFv4.0 and 4.1 parser for Python. The intent of this module is to mimic the csv module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. vcf will attempt to parse the content of each record based on the data types specified in the meta-information lines – specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings. PyVCF3 has been created because the Official PyVCF repository is no longer maintained and do not accept any pull requests. This fork is for python 3 only and has been published on pyPI as PyVCF3.
PycURL/7.45.2-GCCcore-12.2.0
PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features.
Pyomo/6.4.4-foss-2021b
Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models.
Pysam/0.22.1-GCC-13.3.0
Pysam is a python module for reading and manipulating Samfiles. It’s a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Python/3.12.3-GCCcore-13.3.0
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
QIIME2/2020.11
QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
QUAST/5.1.0rc1-foss-2020b
QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison.
Qhull/2020.2-GCCcore-13.2.0
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
RAxML-NG/1.0.3-GCC-10.2.0
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
RDFlib/5.0.0-GCCcore-10.2.0
RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
RE2/2024-03-01-GCCcore-13.2.0
RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library.
RELION/3.1.2-fosscuda-2019b
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
RFdiffusion/1.1.0-foss-2022a-CUDA-11.7.0
RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.
RMBlast/2.14.1-gompi-2023a
RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program ‘rmblastn’ for use with RepeatMasker and RepeatModeler.
RNA-SeQC/2.4.2-foss-2021b
Fast, efficient RNA-Seq metrics for quality control and process optimization
ROSE/1-GCCcore-8.3.0-Python-2.7.16
To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)
RPostgreSQL/0.7-6-foss-2023b
Database interface and ‘PostgreSQL’ driver for ‘R’. This package provides a Database Interface ‘DBI’ compliant driver for ‘R’ to access ‘PostgreSQL’ database systems.
RSeQC/5.0.1-foss-2021b
RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
RStudio-Server/2024.04.1+748-foss-2023b-Java-11-R-4.4.0
This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver –server-daemonize=0 –www-port=8787 If you need a database config one can be created with: MYTMP=mktemp -d && echo -e “provider=sqlite\ndirectory=${MYTMP}/sqlite” > “${MYTMP}/db.conf” and then used with: rserver … –database-config-file=”${MYTMP}/db.conf”
Racon/1.5.0-GCCcore-11.2.0
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
Ray-project/2.6.2-foss-2022b
Ray is a fast and simple framework for building and running distributed applications.
Redis/7.0.12-GCC-12.2.0
Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster.
RegTools/1.0.0-foss-2024a
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
Regenie/3.1.2-GCC-11.2.0
Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center.
RevBayes/1.1.1-GCC-10.2.0
RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics.
Ruby/3.3.0-GCCcore-12.3.0
Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
Rust/1.86.0-GCCcore-13.3.0
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
SAMtools/1.21-GCC-13.3.0
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
SCOTCH/7.0.3-gompi-2022b
Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
SHAPEIT4/4.2.2-foss-2020b
SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.
SLEPc/3.15.1-foss-2021a
SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
SOCI/4.0.3-GCC-11.2.0
SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.
SQANTI3/1.0-foss-2019b-Python-3.7.4
SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, that also includes IsoAnnot and tappAS. Used for new long read-defined transcriptome.
SQLAlchemy/2.0.25-GCCcore-12.3.0
SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.
SRA-Toolkit/3.1.1-gompi-2023b
The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
SSW/1.1-GCCcore-11.2.0
SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
STAR/2.7.11b-GCC-13.3.0
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
STAR-Fusion/1.12.0-foss-2022b
STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
SVIM/2.0.0-foss-2022a
SVIM (pronounced swim) is a structural variant caller for third-generation sequencing reads. It is able to detect and classify the following six classes of structural variation: deletions, insertions, inversions, tandem duplications, interspersed duplications and translocations.
SWIG/4.2.1-GCCcore-13.3.0
SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
SYMPHONY/5.7.2-foss-2023b
SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C.
Salmon/1.10.1-GCC-12.2.0
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
Sambamba/1.0.1-GCC-13.2.0
Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.
ScaLAPACK/2.2.0-gompi-2022a-fb
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
Scalene/1.5.26-GCCcore-12.3.0
Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while delivering far more detailed information.
Seaborn/0.13.2-gfbf-2023a
Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
SeqAn/2.4.0-GCCcore-8.3.0
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.
SeqPrep/1.3.2-GCCcore-8.3.0
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
Seurat/5.1.0-foss-2023b-R-4.4.0
Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.
ShapeMapper2/2.3-GCC-13.3.0
ShapeMapper automates the calculation of RNA chemical probing reactivities from mutational profiling (MaP) experiments, in which chemical adducts on RNA are detected as internal mutations in cDNA through reverse transcription and read out by massively parallel sequencing.
Singularity/3.5.3
Singularity is a portable application stack packaging and runtime utility.
SlamDunk/0.4.3-foss-2021b
SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.
Sniffles/2.6.2-gfbf-2024a
A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.
SpaceRanger/2.0.0-GCC-11.2.0
Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.
SpectrA/1.0.1-GCC-11.2.0
Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.
Stack/2.3.3-x86_64
Stack is a cross-platform program for developing Haskell projects. It is intended for Haskellers both new and experienced.
Stacks/2.53-foss-2019b
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
StringTie/2.2.3-GCC-12.3.0
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts
SuperLU/5.3.0-foss-2021b
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
SuperLU_DIST/8.1.0-foss-2022a
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
Szip/2.1.1-GCCcore-12.2.0
Szip compression software, providing lossless compression of scientific data
TGS-GapCloser/1.2.1-GCCcore-13.3.0
A gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.
TOPAZ/0.2.4-foss-2020b
Topaz is a pipeline for particle picking in cryo-electron micrographs using neural networks and positive-unlabeled learning
TRUST4/1.0.7-GCC-11.2.0
Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information. TRUST4 supports both single-end and paired-end sequencing data with any read length.
TagDust/2.33-GCCcore-8.3.0
Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines.
Tcl/8.6.14-GCCcore-13.3.0
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.
Theano/1.1.2-foss-2020b-PyMC
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
Tk/8.6.14-GCCcore-13.3.0
Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
Tracer/1.7.1
Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.
Trim_Galore/0.6.7-GCCcore-11.2.0
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).
Trimmomatic/0.39-Java-11
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Trinity/2.12.0-foss-2020b
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
UCC/1.3.0-GCCcore-13.3.0
UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.
UCX/1.16.0-GCCcore-13.3.0
Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
UCX-CUDA/1.16.0-GCCcore-13.3.0-CUDA-12.6.0
Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support.
UDUNITS/2.2.28-GCCcore-11.2.0
UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
UnZip/6.0-GCCcore-8.3.0
UnZip is an extraction utility for archives compressed in .zip format (also called “zipfiles”). Although highly compatible both with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s own Zip program, our primary objectives have been portability and non-MSDOS functionality.
VCFtools/0.1.16-GCC-11.2.0
The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
VEP/113.3-GCC-13.3.0
Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.
VSEARCH/2.21.1-GCC-11.2.0
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
VTK/8.2.0-foss-2019b-Python-3.7.4
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
VarScan/2.4.4-Java-11
Variant calling and somatic mutation/CNV detection for next-generation sequencing data
VerifyBamID/2.0.2-foss-2024a
verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps.
ViennaRNA/2.5.1-foss-2021b
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
Vim/9.1.0004-GCCcore-13.2.0
Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor ‘Vi’, with a more complete feature set.
Wayland/1.23.0-GCCcore-13.3.0
Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers.
Waylandpp/1.0.0-GCCcore-12.3.0
Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland.
WebKitGTK+/2.45.2-GCC-12.3.0
WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit’s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions.
WhatsHap/2.2-foss-2023a
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
WiggleTools/1.2.4-GCC-8.3.0
The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon’s rank sum test, etc).
XGBoost/0.90-foss-2019b-Python-3.7.4
XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.
XeniumRanger/4.0.0
The Xenium In Situ software suite is a set of software applications for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
Xerces-C++/3.2.5-GCCcore-13.3.0
Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
Xvfb/21.1.14-GCCcore-13.3.0
Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.
YACS/0.1.8-GCCcore-10.2.0
YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These “configurations” typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network.
Z3/4.13.0-GCCcore-13.2.0
Z3 is a theorem prover from Microsoft Research with support for bitvectors, booleans, arrays, floating point numbers, strings, and other data types. This module includes z3-solver, the Python interface of Z3.
ZeroMQ/4.3.5-GCCcore-13.2.0
ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It’s fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.
Zip/3.0-GCCcore-13.3.0
Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s own UnZip, our primary objectives have been portability and other-than-MSDOS functionality
absl-py/2.1.0-GCCcore-13.3.0
absl-py is a collection of Python library code for building Python applications. The code is collected from Google’s own Python code base, and has been extensively tested and used in production.
alleleCount/4.2.1-GCC-11.2.0
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.
almosthere/2.0.2-GCCcore-10.2.0
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.
alsa-lib/1.2.11-GCCcore-13.2.0
The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.
ancestry/1.0.0-GCCcore-8.3.0-Python-2.7.16
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies from multiple populations. iAdmix Using population allele frequencies for computing individual admixture estimates
anndata/0.11.3-foss-2024a
anndata is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray
annovar/20200607-GCCcore-11.2.0-Perl-5.34.0
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).
ant/1.10.14-Java-21
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.
arcasHLA/0.2.0-foss-2019b-Python-3.7.4
arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
argtable/2.13-GCCcore-8.3.0
Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
aria2/1.35.0-GCCcore-10.2.0
aria2 is a lightweight multi-protocol and multi-source command-line download utility.
arpack-ng/3.9.1-foss-2023b
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
assimp/5.3.1-GCCcore-13.2.0
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.
astropy/6.0.1-foss-2023a
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.
attrdict3/2.0.2-GCCcore-12.3.0
AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.
bcl-convert/4.0.3-2el7.x86_64
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.
bcl2fastq2/2.20.0-foss-2019b
bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
bcrypt/4.1.3-GCCcore-13.2.0
Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt)
beagle-lib/4.0.1-GCC-12.3.0-CUDA-12.1.1
beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
bgen/4.1.3-GCCcore-10.2.0
A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3.
biom-format/2.1.16-foss-2023b
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.
blake3/0.4.1-GCCcore-12.3.0
Python bindings for BLAKE3. A cryptographic hash function that is Much faster than MD5, SHA-1, SHA-2, SHA-3, and BLAKE2.
boto3/1.28.70-GCCcore-12.3.0
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.
brotli/1.0.9-GCC-8.3.0
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.
bsddb3/6.2.9-GCCcore-10.2.0
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.
bubblewrap/0.11.1-GCCcore-12.3.0
Unprivileged sandboxing tool. bubblewrap runs an application in a sandbox, where it has restricted access to parts of the operating system or user data such as the home directory. Used by Flatpak and similar projects.
bwidget/1.9.16-GCCcore-12.3.0
The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.
bx-python/0.13.0-foss-2023b
The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
bzip2/1.0.8-GCCcore-13.3.0
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.
cURL/8.7.1-GCCcore-13.3.0
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.
cairo/1.18.0-GCCcore-13.2.0
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
cas-offinder/2.4.1-foss-2023b
Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
ccache/4.9-GCCcore-12.3.0
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
cctbx-base/2020.8-fosscuda-2020b
The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific applications.
cellranger/3.1.0
Chromium Single Cell Software Suite is a set of software applications for analyzing and visualizing single cell 3’ RNA-seq data produced by the 10x Genomics Chromium Platform.
cellsnp-lite/1.2.3-GCC-13.2.0
Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each allele of given or detected SNPs.
cffi/1.16.0-GCCcore-13.3.0
C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation.
cget/0.2.0-foss-2021b
Cmake package retrieval. This can be used to download and install cmake packages
cisTEM/1.0.0-beta-foss-2019b
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
cnpy/master-GCC-11.2.0
cnpy lets you read and write NumPy arrays saved as npy file formats in C++.
configurable-http-proxy/4.5.5-GCCcore-12.2.0
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.
cooltools/0.7.1-foss-2024a
cooltools provides a suite of computational tools with a paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation.
cppy/1.2.1-GCCcore-12.3.0
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.
cromwell/87
Scientific workflow engine designed for simplicity & scalability.
cryptography/42.0.8-GCCcore-13.3.0
cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.
cuDNN/9.5.0.50-CUDA-12.6.0
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
cupcake/0.0.4-foss-2019b-Python-3.7.4
Cupcake is a thin layer over CMake and Conan that tries to offer a better user experience in the style of Yarn or Poetry.
cutadapt/5.0-GCCcore-13.2.0
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cuteSV/2.1.2-foss-2024a
cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.
dask/2024.9.1-gfbf-2024a
Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
datamash/1.8-GCCcore-11.2.0
GNU datamash performs basic numeric, textual and statistical operations on input data files
deepTools/3.5.4.post1-gfbf-2022b
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.
deepdiff/6.7.1-GCCcore-12.3.0
DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.
delly/0.8.3
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
dill/0.3.9-GCCcore-13.3.0
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.
dm-haiku/0.0.12-foss-2023a-CUDA-12.1.1
Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural network library for TensorFlow.
dm-tree/0.1.8-GCCcore-12.3.0
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.
dms_tools2/2.6.11-foss-2020b
dms_tools2 is a software package for analyzing deep mutational scanning data. It is tailored to analyze libraries created using comprehensive codon mutagenesis of protein-coding of genes.
dotNET-Core/8.0.411
.NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime.
dotNET-SDK/3.1.300-linux-x64
.NET is a free, cross-platform, open source developer platform for building many different types of applications.
e3nn/0.3.3-foss-2022a-CUDA-11.7.0
Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3).
easel/0.48-GCC-12.2.0
Easel supports computational analysis of biological sequences using probabilistic models.
edlib/1.3.9.post1-GCC-13.3.0
Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
eggnog-mapper/2.1.7-foss-2021b
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.
einops/0.8.0-GCCcore-13.2.0
Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.
enchant-2/2.6.5-GCCcore-12.3.0
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.
epiScanpy/0.4.0-foss-2023a
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].
expat/2.6.2-GCCcore-13.3.0
Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags).
expect/5.45.4-GCCcore-9.3.0
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.
expecttest/0.2.1-GCCcore-13.2.0
This library implements expect tests (also known as “golden” tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.
factera/1.4.4-foss-2019b-Perl-5.30.0
(Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm) is a tool for detection of genomic fusions in paired-end targeted (or genome-wide) sequencing data.
faiss/1.7.3-foss-2021b-CUDA-11.4.1
FAISS (Facebook AI Similarity Search) is a library that allows developers to quickly search for embeddings of multimedia documents that are similar to each other.
fast5/0.6.5
A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
fastNGSadmix/dda93a4-GCC-10.2.0
Program for infering admixture proportions and doing PCA with a single NGS sample. Inferences based on reference panel.
fastp/0.23.4-GCC-13.2.0
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
fastq-tools/0.8.3-GCC-11.2.0
This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.
ffnvcodec/12.1.14.0
FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).
fgbio/2.0.2
A set of tools to analyze genomic data with a focus on Next Generation Sequencing.
fhCellRanger/7.1.0
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.
fhCellpose/0.6.5-fosscuda-2020b
Cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu.
fhDev/GCCcore-8.3.0
fhDev Fred Hutch Development environment is a collection of development tools that will work with LMOD modules for a given environment.
fhR/4.4.1-foss-2023b
R is a free software environment for statistical computing and graphics.
fhSeurat/4.1.1-foss-2021b-R-4.2.0
Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. fhSeurat module has additional Bioconductor packages for single-cell analysis.
fhStack/2.3.3-x86_64
Stack is a cross-platform program for developing Haskell projects. It is intended for Haskellers both new and experienced.
file/5.43-GCCcore-13.2.0
The file command is ‘a file type guesser’, that is, a command-line tool that tells you in words what kind of data a file contains.
filezilla/3.62.2-GCC-11.2.0
FileZilla Client is a fast and reliable cross-platform FTP, FTPS and SFTP client with lots of useful features and an intuitive graphical user interface.
flex/2.6.4-GCCcore-11.2.0
Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.
fontconfig/2.15.0-GCCcore-13.3.0
Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
fonttools/4.53.1-GCCcore-13.3.0
fontTools is a library for manipulating fonts, written in Python. The project includes the TTX tool, that can convert TrueType and OpenType fonts to and from an XML text format, which is also called TTX. It supports TrueType, OpenType, AFM and to an extent Type 1 and some Mac-specific formats.
foss/2024a
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
fosscuda/2020b
GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
freeglut/3.4.0-GCCcore-12.3.0
freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
freetds/1.2-GCCcore-10.2.0
FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases.
freetype/2.13.2-GCCcore-13.2.0
FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
future/0.18.3-foss-2021b
python-future is the missing compatibility layer between Python 2 and Python 3.
gawk/5.1.0-GCC-10.2.0
The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
gc/8.2.4-GCCcore-12.3.0
The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
gcccuda/2020b
GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
gcloud/439.0.0
Libraries and tools for interacting with Google Cloud products and services.
gdc-client/2.3
The GDC provides a standard client-based mechanism supporting high-performance data downloads and submission.
gettext/0.22.5-GCCcore-13.3.0
GNU ‘gettext’ is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
gfbf/2024a
GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.
gffread/0.12.7-GCCcore-12.3.0
GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
gflags/2.2.2-GCCcore-8.3.0
The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.
ggVennDiagram/3484e8-foss-2019b-R-4.0.2
A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
giflib/5.2.1-GCCcore-11.3.0
giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.
giggle/master-foss-2020b
GIGGLE is a genomics search engine that identifies and ranks the significance of shared genomic loci between query features and thousands of genome interval files.
git/2.45.1-GCCcore-13.3.0
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
git-lfs/2.11.0
Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
glew/2.2.0-GCCcore-11.2.0-glx
The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform.
gompi/2024a
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
gompic/2020b
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
gperf/3.1-GCCcore-11.2.0
GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
gperftools/2.13-GCCcore-13.2.0
gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.
graphite2/1.3.14-GCCcore-12.2.0
Graphite is a “smart font” system developed specifically to handle the complexities of lesser-known languages of the world.
groff/1.23.0-GCCcore-13.3.0
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.
grpcio/1.70.0-GCCcore-13.3.0
gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems.
gsutil/5.10-GCCcore-11.2.0
gsutil is a Python application that lets you access Cloud Storage from the command line.
gzip/1.13-GCCcore-13.2.0
gzip (GNU zip) is a popular data compression program as a replacement for compress
h5netcdf/1.2.0-foss-2023a
A Python interface for the netCDF4 file-format that reads and writes local or remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata netCDF library.
h5py/3.12.1-foss-2024a
HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
hatch-jupyter-builder/0.9.1-GCCcore-13.2.0
Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.
hatchling/1.24.2-GCCcore-13.3.0
Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager.
help2man/1.49.3-GCCcore-13.2.0
help2man produces simple manual pages from the ‘–help’ and ‘–version’ output of other commands.
hiredis/1.2.0-GCCcore-12.3.0
Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command.
hmmlearn/0.3.2-gfbf-2023a
hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models
hunspell/1.7.2-GCCcore-12.3.0
Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding.
hwloc/2.10.0-GCCcore-13.3.0
The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, …) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
hyperfreq/1.2.0-foss-2020b
Hypermutation analysis software using BetaRat distribution for Bayesian analysis of the relative probability ratio (RPR) of observing mutations in two contexts. Includes Alnclst, for clustering pre-aligned nucleotide sequences.
hypothesis/6.103.1-GCCcore-13.3.0
Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.
iVar/1.3.2-GCC-11.2.0
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
icav2/2.37.0
icav2 is a CLI for Illumina® Connected Analytics.
igraph/0.10.12-foss-2023b
igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.
imageio/2.36.1-gfbf-2024a
Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats.
index-hopping-filter/1.0.1
index-hopping-filter is a tool that filters index hopped reads from a set of demultiplexed samples. The tool detects and removes likely index hopped reads from demultiplexed FASTQs, and in turn emits new, filtered, FASTQs with similar file and directory layout as the inputs, suitable for use with cellranger count and cellranger vdj.
infercnvpy/0.4.3-foss-2023a
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
interop/1.1.10-foss-2019b-Python-3.7.4
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.
intltool/0.51.0-GCCcore-10.3.0
intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
itpp/4.3.1-foss-2019b
IT++ is a C++ library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications.
jax/0.4.25-foss-2023a
Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
jbigkit/2.1-GCCcore-10.2.0
JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.
jemalloc/5.3.0-GCCcore-12.2.0
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
json-c/0.17-GCCcore-13.3.0
JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.
jupyter-server/2.14.2-GCCcore-13.3.0
The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.
jupyter-server-proxy/3.2.2-GCCcore-12.2.0
Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example.
kallisto/0.50.1-foss-2022b
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
kineto/0.4.0-GCC-12.3.0
A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters
king/2.2.5
KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.
kneaddata/0.12.0-foss-2022a
KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
leidenalg/0.10.2-foss-2023b
Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
lftp/4.9.1-GCCcore-8.3.0
LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.
libaec/1.0.6-GCCcore-12.3.0
Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
libasound/1.2.2-GCCcore-8.3.0
The libnl suite is a collection of libraries providing APIs to netlink protocol based Linux kernel interfaces.
libavif/1.0.4-GCCcore-12.3.0
This library aims to be a friendly, portable C implementation of the AV1 Image File Format, as described here: https://aomediacodec.github.io/av1-avif/
libbacktrace/20240505-GCC-12.3.0
A C library that may be linked into a C/C++ program to produce symbolic backtraces Initially written by Ian Lance Taylor iant@golang.org. This is version 1.0. It is likely that this will always be version 1.0.
libcap/2.69-GCCcore-12.3.0
libcap is a library for getting and setting POSIX.1e (formerly POSIX 6) draft 15 capabilities. Required as a dependency for bubblewrap and other sandboxing tools.
libcerf/2.4-GCC-13.2.0
libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.
libedit/20191231-GCC-8.3.0
This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline.
libev/4.33-GCC-11.2.0
A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs.
libevent/2.1.12-GCCcore-13.2.0
The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
libfabric/1.21.0-GCCcore-13.3.0
Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.
libffi/3.4.5-GCCcore-13.3.0
The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
libfilezilla/0.40.0-GCC-11.2.0
libfilezilla is a small and modern C++ library, offering some basic functionality to build high-performing, platform-independent programs.
libgit2/1.8.1-GCCcore-13.3.0
libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.
libglvnd/1.7.0-GCCcore-13.2.0
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libiconv/1.17-GCCcore-13.3.0
Libiconv converts from one character encoding to another through Unicode conversion
libidn/1.38-GCCcore-11.2.0
GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn’s purpose is to encode and decode internationalized domain names.
libidn2/2.3.7-GCCcore-12.3.0
Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.
libjpeg-turbo/3.0.1-GCCcore-13.2.0
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
libmicrohttpd/0.9.73-GCCcore-10.2.0
GNU libmicrohttpd is a small C library that is supposed to make it easy to run an HTTP server as part of another application.
libogg/1.3.5-GCCcore-13.3.0
Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
libopus/1.5.2-GCCcore-13.3.0
Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec.
libpthread-stubs/0.4-GCCcore-8.3.0
The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
libreadline/8.2-GCCcore-13.2.0
The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
libsndfile/1.2.2-GCCcore-13.3.0
Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
libsodium/1.0.20-GCCcore-13.3.0
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
libtasn1/4.19.0-GCCcore-12.3.0
Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package.
libtool/2.4.7
GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
libunistring/1.1-GCCcore-12.3.0
This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libunwind/1.8.1-GCCcore-13.3.0
The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
libvips/8.15.2-GCC-12.3.0
libvips is a demand-driven, horizontally threaded image processing library.
libvorbis/1.3.7-GCCcore-13.3.0
Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
libwebp/1.4.0-GCCcore-13.3.0
WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.
libwpe/1.14.2-GCCcore-12.3.0
WPE is the reference WebKit port for embedded and low-consumption computer devices. It has been designed from the ground-up with performance, small footprint, accelerated content rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices.
lit/18.1.8-GCCcore-13.3.0
lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and providing indication of failures.
lxml/5.3.0-GCCcore-13.3.0
The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
lz4/1.9.4-GCCcore-12.2.0
LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.
magma/2.7.2-foss-2023a-CUDA-12.1.1
The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.
makeinfo/7.1-GCCcore-13.3.0
makeinfo is part of the Texinfo project, the official documentation format of the GNU project.
manta/1.6.0
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.
matplotlib/3.9.2-gfbf-2024a
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
maturin/1.6.0-GCCcore-13.3.0
This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support.
minimap2/2.29-GCCcore-13.3.0
Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.
ml_dtypes/0.5.0-gfbf-2024a
ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including: bfloat16: an alternative to the standard float16 format float8_*: several experimental 8-bit floating point representations including: float8_e4m3b11fnuz float8_e4m3fn float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz
monocle3/0.2.2-foss-2019b-R-4.0.2
Single-cell transcriptome sequencing (sc-RNA-seq) experiments allow us to discover new cell types and help us understand how they arise in development. The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
monolix/2019R2
Monolix performs non-linear mixed effects modeling (NLME) for pharmacometrics.
motif/2.3.8-GCCcore-11.2.0
Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.
mpath/1.1.3-GCCcore-11.3.0
For now it’s quit simple and get_path_info() method returns information about given path. It can be either a directory or a file path.
mpi4py/4.0.1-gompi-2024a
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
mrcfile/1.3.0-fosscuda-2020b
mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions.
msisensor-pro/1.3.0-GCC-13.3.0
MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input.
nbclassic/1.0.0-GCCcore-12.3.0
NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking.
ncbi-vdb/3.1.1-gompi-2023b
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
ncdf4/1.17-foss-2019b
ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files
ncdu/1.15.1-GCCcore-8.3.0
Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don’t have an entire graphical setup available, but it is a useful tool even on regular desktop systems.
ncurses/6.5
The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
ndindex/1.7-foss-2023a
ndindex is a library that allows representing and manipulating objects that can be valid indices to numpy arrays, i.e., slices, integers, ellipses, None, integer and boolean arrays, and tuples thereof.
netCDF/4.9.2-gompi-2024a
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netMHCIIpan/4.3
The NetMHCIIpan-4.3 server predicts peptide binding to HLA class II molecules using Artificial Neural Networks (ANNs). It is trained on an extensive dataset of over 650,000 measurements of Binding Affinity (BA) and Eluted Ligand mass spectrometry (EL), covering the three human MHC class II isotypes HLA-DR, HLA-DQ, HLA-DP, as well as mouse (H-2) and bovine (BoLA-DRB3) molecules.
netMHCpan/4.1b
The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs).
nettle/3.10-GCCcore-13.3.0
Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, …), in applications like LSH or GNUPG, or even in kernel space.
networkx/3.4.2-gfbf-2024a
NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
nextflow/24.04.3
Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows. It supports deploying workflows on a variety of execution platforms including local, HPC schedulers, AWS Batch, Google Genomics Pipelines, and Kubernetes.
nghttp2/1.62.0-GCC-12.3.0
This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API.
nghttp3/1.3.0-GCCcore-12.3.0
nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation.
ngtcp2/1.5.0-GCC-12.3.0
‘Call it TCP/2. One More Time.’ ngtcp2 project is an effort to implement RFC9000 QUIC protocol.
nodejs/20.13.1-GCCcore-13.3.0
Node.js is a platform built on Chrome’s JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
nsync/1.29.2-GCCcore-13.2.0
nsync is a C library that exports various synchronization primitives, such as mutexes
nullarbor/2.0.20191013
Pipeline to generate complete public health microbiology reports from sequenced isolates
numactl/2.0.18-GCCcore-13.3.0
The numactl program allows you to run your application program on specific cpu’s and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
numba/0.60.0-foss-2024a
Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
numexpr/2.7.1-foss-2019b-Python-2.7.16
The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime.
oarfish/0.6.5-GCCcore-13.2.0
oarfish is a program for quantifying transcript-level expression from long-read (i.e. Oxford nanopore cDNA and direct RNA and PacBio) sequencing technologies.
oncosnpseq/2.01
OncoSNP-SEQ is an analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.
ont-guppy-cpu/2.3.7
Guppy is a production basecaller provided by Oxford Nanopore, and uses a command-line interface.
p11-kit/0.25.3-GCCcore-12.3.0
Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they’re discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process.
paramiko/3.5.1-GCCcore-13.2.0
Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol, providing both client and server functionality. It provides the foundation for the high-level SSH library Fabric, which is what we recommend you use for common client use-cases such as running remote shell commands or transferring files.
petsc4py/3.15.0-foss-2021a
petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation.
philosopher/3.3.11
Philosopher provides easy access to third-party tools and custom algorithms allowing users to develop proteomics analysis, from Peptide Spectrum Matching to annotated protein reports. Philosopher is also tuned for Open Search analysis, providing a modified version of the prophets for peptide validation and protein inference. To this date, Philosopher is the only proteomics toolkit that allows you to process and analyze close and open search results.
picard/2.25.1-Java-11
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
pigz/2.8-GCCcore-13.2.0
pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.
pipdeptree/0.13.2-foss-2019b-Python-3.7.4
pipdeptree is a command line utility for displaying the installed python packages in form of a dependency tree. It works for packages installed globally on a machine as well as in a virtualenv.
pipseeker/3.3.0
PIPseeker(TM) analyzes single-cell data obtained with Fluent BioSciences’ proprietary PIPseq™ 3ʹ Single Cell RNA (scRNA-seq) Kits.
pixman/0.43.4-GCCcore-13.3.0
Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
pkg-config/0.29.2-GCCcore-10.3.0
pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).
pkgconf/2.2.0-GCCcore-13.3.0
pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.
plinkliftover/0.3.0-foss-2022b
PLINKLiftOver is a utility enabling liftOver to work on genomics files from PLINK, allowing one to update the coordinates from one genome reference version to another.
pocl/4.0-GCC-12.2.0
PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported).
poetry/1.8.3-GCCcore-13.3.0
Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere.
polars/0.20.2-gfbf-2023a
Polars is a blazingly fast DataFrame library for manipulating structured data. The core is written in Rust and this module provides its interface for Python.
popscle/0.1-beta-foss-2019b
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
pplacer/1.1.alpha19
Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
preCICE/2.5.0-foss-2022a
preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations, including, but not restricted to fluid-structure interaction and conjugate heat transfer simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. This allows for the high flexibility that is needed to keep a decent time-to-solution for complex multi-physics scenarios.
prodigal/2.6.3-GCCcore-11.2.0
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
prokka/1.14.5-gompi-2019b
Prokka is a software tool for the rapid annotation of prokaryotic genomes.
prompt-toolkit/3.0.36-GCCcore-13.3.0
prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.
protobuf/28.0-GCCcore-13.3.0
Protocol Buffers (a.k.a., protobuf) are Google’s language-neutral, platform-neutral, extensible mechanism for serializing structured data.
protobuf-c/1.3.3-GCCcore-8.3.0
This is protobuf-c, a C implementation of the Google Protocol Buffers data serialization format
pySCENIC/20250316-foss-2022b
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
pyaml/21.10.1-GCC-11.2.0
PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc).
pybedtools/0.9.1-foss-2023a
pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
pybind11/2.13.6-GCC-13.3.0
pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
pycisTarget/1.0.2-foss-2022b
pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.
pyclone/0.13.1-foss-2019b-Python-2.7.16
PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination.
pyclone-vi/0.1.0-foss-2019b-Python-3.7.4
PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination.
pyro-ppl/1.9.0-foss-2023a
Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch.
pyrovelocity/0.4.0-beta.4-foss-2024a-CUDA-12.4.0
is a library for probabilistic inference in minimal models approximating gene expression dynamics from, possibly multimodal, single-cell sequencing data. It provides posterior estimates of gene expression parameters, predictive estimates of gene expression states, and local estimates of cell state transition probabilities.
pytest/8.3.3-GCCcore-13.3.0
The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries.
pytest-astropy/0.11.0-gfbf-2023a
This is a meta-package that pulls in the dependencies that are used by astropy and some affiliated packages for testing.
pytest-shard/0.1.2-GCCcore-13.2.0
pytest plugin to support parallelism across multiple machines. Shards tests based on a hash of their test name enabling easy parallelism across machines, suitable for a wide variety of continuous integration services. Tests are split at the finest level of granularity, individual test cases, enabling parallelism even if all of your tests are in a single file (or even single parameterized test method).
pytest-workflow/2.1.0-GCCcore-13.3.0
Configure workflow/pipeline tests using yaml files. pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by using YAML files for the test configuration. Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, pytest-workflow makes testing easy. pytest-workflow is build on top of the pytest test framework.
pytest-xdist/3.6.1-GCCcore-13.2.0
xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * –looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters.
python-igraph/0.11.4-foss-2023a
Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.
python-isal/1.7.0-GCCcore-13.3.0
Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library.
quarto/1.5.57-x64
An open-source scientific and technical publishing system.
rMATS-turbo/4.3.0-gfbf-2024a
rMATS turbo is the C/Cython version of rMATS (refer to https://rnaseq-mats.sourceforge.io).
re2c/3.1-GCCcore-13.2.0
re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.
rgdal/1.4-8-foss-2019b-R-4.0.2
Provides bindings to the ‘Geospatial’ Data Abstraction Library (‘GDAL’) (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the ‘PROJ.4’ library.
scCODA/0.1.9-foss-2023a
scCODA allows for identification of compositional changes in high-throughput sequencing count data, especially cell compositions from scRNA-seq.
scVelo/0.3.1-foss-2023a
scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling.
scanpy/1.10.4-foss-2024a
Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
scenicplus/1.0.0-foss-2022b
SCENIC+ is a python package to build enhancer driven gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
scib/1.1.4-foss-2023a
Benchmarking atlas-level data integration in single-cell genomics.
scikit-bio/0.6.0-foss-2023a
scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.
scikit-build/0.17.6-GCCcore-13.3.0
Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.
scikit-build-core/0.10.6-GCCcore-13.3.0
Scikit-build-core is a complete ground-up rewrite of scikit-build on top of modern packaging APIs. It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake.
scikit-learn/1.6.1-gfbf-2024a
Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.
scikit-optimize/0.9.0-foss-2021b
Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions.
scipy/1.4.1-foss-2019b-Python-3.7.4
SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python.
scvi-tools/1.1.2-foss-2023a
scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
seq2HLA/2.3-foss-2019b-Python-2.7.16
In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
seqtk/1.3-GCC-8.3.0
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
seqtools/4.44.1-foss-2019b
The SeqTools package contains three tools for visualising sequence alignments: Blixem, Dotter and Belvu.
sequenza-utils/3.0.0-GCCcore-8.3.0-Python-3.7.4
Sequenza is a software for the estimation and quantification of purity/ploidy and copy number alteration in sequencing experiments of tumor samples. Sequenza-utils provide command lines programs to transform common NGS file format
slepc4py/3.15.1-foss-2021a
Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations.
snakemake/7.32.3-foss-2022b
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
snappy/1.2.1-GCCcore-13.3.0
Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
snippy/4.6.0-foss-2019b-Perl-5.30.0
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment.
soap-hla/1.0.0-GCCcore-12.2.0
SOAP-HLA is a flow of sequencing data analysis pipeline to type all of the HLA genes in IMGT/HLA database using capture sequenced data or WGS data with high accuracy.
spams/2.6.5.4-foss-2021b
SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems.
span-lite/0.10.3-GCC-11.2.0
span lite is a single-file header-only library to provide a bounds-safe view for sequences of objects. The library provides a C++20-like span for use with C++98 and later.
spektral/1.1.0-foss-2021b-CUDA-11.4.1
Spektral is a Python library for graph deep learning. The main goal of this project is to provide a simple but flexible framework for creating graph neural networks (GNNs).
spglib-python/1.16.0-foss-2020b
Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
splitpipe/1.3.1-foss-2023b
splitpipe tool from Parse Biosciences. The pipeline takes FASTQ files and delivers processed data in the form of a cell-gene count matrix, which serves as the input for various open sources tools such as scanpy and seuratProcess sequencing results with our pipeline. A Parse Bioscience login ID is required to download
spoa/4.1.0-GCC-13.3.0
Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences
sprocket/0.23.0
Sprocket is a bioinformatics workflow orchestration engine.
starcode/1.4-GCC-11.2.0
Starcode is a DNA sequence clustering software. Starcode clustering is based on all pairs search within a specified Levenshtein distance (allowing insertions and deletions), followed by a clustering algorithm: Message Passing, Spheres or Connected Components.
statsmodels/0.14.4-gfbf-2024a
Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.
sympy/1.12-gfbf-2023b
SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.
sysbench/1.0.20-GCC-12.2.0
sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex workloads that do not involve a database server.
tbb/2021.13.0-GCCcore-13.3.0
Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.
tbl2asn/20220427-linux64
Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
tensorboard/2.18.0-gfbf-2024a
TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs.
tensorstore/0.1.65-foss-2023a
TensorStore is an open-source C++ and Python software library designed for storage and manipulation of large multi-dimensional arrays.
texlive/20210324-GCC-11.2.0
TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated.
tmux/3.4-GCCcore-13.2.0
tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.
umap-learn/0.5.7-foss-2024a
Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
unixODBC/2.3.12-GCC-13.2.0
unixODBC provides a uniform interface between application and database driver
utf8proc/2.9.0-GCCcore-13.2.0
utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.
uv/0.6.4
A single tool to replace pip, pip-tools, pipx, poetry, pyenv, twine, virtualenv, and more.
vcf2maf/1.6.19
vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.
vcflib/1.0.1-GCCcore-8.3.0
vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.
velocyto.R/0.6-foss-2019b-R-4.0.2
velocyto (velox + κύτος, quick cell) is a package for the analysis of expression dynamics in single cell RNA seq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols (see pre-print below for more information).
verifyBamID/1.1.3-foss-2023b
verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps.
versioningit/3.1.2-GCCcore-13.3.0
versioningit is yet another Python packaging plugin for automatically determining your package’s version based on your version control repository’s tags. Unlike others, it allows easy customization of the version format and even lets you easily override the separate functions used for version extraction & calculation.
wget/1.24.5-GCCcore-12.3.0
GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
wpebackend-fdo/1.14.2-GCCcore-12.3.0
WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance.
wrapt/1.16.0-gfbf-2024a
The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.
wxPython/4.2.1-foss-2023a
Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code.
wxWidgets/3.2.2.1-GCCcore-12.2.0
wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform’s native API rather than emulating the GUI.
x264/20231019-GCCcore-13.2.0
x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
x265/3.5-GCCcore-12.2.0
x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.
xarray/2023.9.0-gfbf-2023a
xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.
xprop/1.2.5-GCCcore-10.2.0
The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.
xxd/9.1.1275-GCCcore-13.3.0
xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.
zarr/2.18.4-foss-2024a
Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.
zlib/1.3.1
zlib is designed to be a free, general-purpose, legally unencumbered – that is, not covered by any patents – lossless data-compression library for use on virtually any computer hardware and operating system.
zstd/1.5.6-GCCcore-13.3.0
Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.