| R |
lang |
R is a free software environment for statistical computing and graphics. |
| ant |
devel |
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. |
| apptainer |
tools |
Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal
of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should
be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux
version differences between the source and target systems. |
| aspera-connect |
tools |
Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and
downloads with an Aspera transfer server. |
| assimp |
vis |
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.
|
| bcftools |
bio |
SAMtools is a suite of programs for interacting with high-throughput sequencing data.
BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence
variants |
| bedtools |
bio |
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. |
| binutils |
tools |
binutils: GNU binary utilities |
| bison |
lang |
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. |
| blast |
bio |
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. |
| boost |
devel |
Boost provides free peer-reviewed portable C++ source libraries. |
| bowtie2 |
bio |
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. |
| bwa |
bio |
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
relatively short nucleotide sequences against a long reference sequence such as the human genome. |
| bzip2 |
tools |
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. |
| cairo |
vis |
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 |
| cereal |
lib |
cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly
turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be
fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or
used standalone. |
| circos |
bio |
Circos is a software package for visualizing data and information.
It visualizes data in a circular layout - this makes Circos ideal for exploring
relationships between objects or positions. |
| cmake |
devel |
CMake, the cross-platform, open-source build system. CMake is a family of
tools designed to build, test and package software.
|
| code-server |
tools |
Run VS Code on any machine anywhere and access it in the browser. |
| comp2comp |
bio |
Comp2Comp is a library for extracting clinical insights from computed tomography scans. |
| conn-toolbox |
bio |
CONN is an open-source, SPM-based, cross-platform software for the computation,
display and analysis of functional connectivity from brain fMRI sequences
(functional Magnetic Resonance Imaging). It supports analyses of both resting
state (rsfMRI) as well as task designs. |
| connectomeworkbench |
bio |
Connectome Workbench is an open source, freely available visualization
and discovery tool used to map neuroimaging data, especially data generated by the
Human Connectome Project. |
| ctakes |
data |
Apache cTAKES is a natural language processing system for extraction of information from electronic medical record clinical free-text. |
| cuda |
system |
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. |
| curl |
tools |
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.
|
| cutadapt |
bio |
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
| dbus |
devel |
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.
|
| double-conversion |
lib |
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. |
| doxygen |
devel |
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. |
| dsi-studio |
bio |
DSI Studio is a lightweight and user-friendly software for diffusion MRI analysis, tractography, and connectome mapping. |
| eigen |
math |
Eigen is a C++ template library for linear algebra:
matrices, vectors, numerical solvers, and related algorithms. |
| expat |
tools |
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). |
| fastqc |
bio |
FastQC is a Java application which takes a FastQ file and runs a series
of tests on it to generate a comprehensive QC report. |
| ffmpeg |
vis |
A complete, cross-platform solution to record, convert and stream audio and video. |
| fftw |
numlib |
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. |
| fiji |
tools |
Fiji is an image processing distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. |
| fontconfig |
vis |
Fontconfig is a library designed to provide system-wide font configuration,
customization and application access.
|
| freetype |
vis |
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.
|
| fribidi |
lang |
The Free Implementation of the Unicode Bidirectional Algorithm. |
| fsl |
data |
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. |
| gatk |
bio |
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 |
compiler |
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,...). |
| gd |
bio |
GD.pm - Interface to Gd Graphics Library |
| gdc-client |
tools |
The gdc-client provides several convenience functions over
the GDC API which provides general download/upload via HTTPS. |
| gettext |
tools |
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 |
| giflib |
lib |
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. |
| glib |
vis |
GLib is one of the base libraries of the GTK+ project |
| go |
lang |
Go is an open source programming language that makes it easy to build
simple, reliable, and efficient software. |
| gobject-introspection |
devel |
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. |
| gompi |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit,
including OpenMPI for MPI support. |
| goolf |
toolchain |
GNU Compiler Collection (GCC) based compiler toolchain,
including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
| gperf |
devel |
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. |
| gsl |
numlib |
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. |
| harfbuzz |
vis |
HarfBuzz is an OpenType text shaping engine. |
| hdf5 |
data |
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. |
| hisat2 |
bio |
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). |
| htslib |
bio |
A C library for reading/writing high-throughput sequencing data.
This package includes the utilities bgzip and tabix |
| hwloc |
system |
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.
|
| icu |
lib |
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode
and Globalization support for software applications. |
| idl |
data |
IDL is an interpreted programming language used to create analyses
and visualizations of numerical data. |
| intltool |
lang |
The Intltool is an internationalization tool used for extracting translatable strings from source files, collecting the extracted strings with messages from traditional source files, and merging the translations into .xml, .desktop and .oaf files. |
| jasper |
vis |
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 |
lang |
Java Platform, Standard Edition (Java SE) lets you develop and deploy
Java applications on desktops and servers. |
| jbigkit |
vis |
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 |
lib |
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and
scalable concurrency support. |
| junit |
devel |
A programmer-oriented testing framework for Java. |
| jupyterlab |
tools |
Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
|
| kallisto |
bio |
Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. |
| knime |
data |
KNIME is an analytics platform for data mining. |
| lame |
data |
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. |
| leptonica |
vis |
Leptonica is a collection of pedagogically-oriented open source software
that is broadly useful for image processing and image analysis applications. |
| libarchive |
tools |
Multi-format archive and compression library
|
| libdeflate |
system |
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. |
| libevent |
lib |
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 |
lib |
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 |
lib |
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. |
| libgd |
lib |
GD is an open source code library for the dynamic creation of images by programmers. |
| libiconv |
lib |
Libiconv converts from one character encoding to another through Unicode conversion |
| libjpeg-turbo |
lib |
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.
|
| libpciaccess |
system |
Generic PCI access library. |
| libpng |
lib |
libpng is the official PNG reference library |
| libtiff |
lib |
tiff: Library and tools for reading and writing TIFF data files |
| libwebp |
lib |
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. |
| libxml2 |
lib |
Libxml2 is the XML C parser and toolchain developed for the Gnome project
(but usable outside of the Gnome platform).
|
| manta |
bio |
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. |
| matlab |
math |
MATLAB is a high-level language and interactive environment
that enables you to perform computationally intensive tasks faster than with
traditional programming languages such as C, C++, and Fortran. |
| mcr |
math |
The MATLAB Runtime is a standalone set of shared libraries
that enables the execution of compiled MATLAB applications
or components on computers that do not have MATLAB installed. |
| meson |
tools |
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. |
| miniforge |
lang |
Miniforge is a free minimal installer for conda and Mamba specific
to conda-forge. |
| mrtrix3 |
bio |
MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. It is designed with consistency, performance, and stability in mind, and is freely available under an open-source license. It is developed and maintained by a team of experts in the field, fostering an active community of users from diverse backgrounds. |
| mrtrix3tissue |
bio |
MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software. |
| mutsigcv |
bio |
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. |
| nasm |
lang |
NASM: General-purpose x86 assembler |
| ncbi-vdb |
bio |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for
using data in the INSDC Sequence Read Archives. |
| ndadownloadmanager |
bio |
The new Download Manager tool is an electron client that was developed with the main philosophy of making the NDA Download Manager extremely easy to use. |
| nextflow |
tools |
Nextflow is a reactive workflow framework and a programming DSL
that eases writing computational pipelines with complex data |
| ninja |
tools |
Ninja is a small build system with a focus on speed. |
| nodejs |
lang |
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. |
| nspr |
lib |
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level
and libc-like functions. |
| nss |
lib |
Network Security Services (NSS) is a set of libraries designed to support cross-platform development
of security-enabled client and server applications. |
| openblas |
numlib |
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. |
| openmpi |
mpi |
The Open MPI Project is an open source MPI-3 implementation. |
| pcre2 |
devel |
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax
and semantics as Perl 5.
|
| peakseq |
bio |
PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq
experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from
a control experiment and outputs a file with peak regions ranked with increasing Q-values. |
| perl |
lang |
Larry Wall's Practical Extraction and Report Language |
| picard |
bio |
A set of tools (in Java) for working with next generation sequencing data in the BAM format. |
| plink |
bio |
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. |
| pmix |
lib |
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 - in fact, PMIx fully supports both of the existing PMI-1
and PMI-2 APIs - but rather to (a) augment and extend those APIs to
eliminate some current restrictions that impact scalability, and (b)
provide a reference implementation of the PMI-server that demonstrates
the desired level of scalability.
|
| postgresql |
data |
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. |
| python |
lang |
Python is a programming language that lets you work
more effectively. |
| pytorch |
data |
PyTorch is a deep learning framework that puts Python first. It provides Tensors and Dynamic neural networks in Python with strong GPU acceleration.
|
| re2c |
tools |
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. |
| rstudio-server |
lang |
RStudio is an integrated development environment (IDE) for the R programming language. |
| salmon |
bio |
Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. |
| samtools |
bio |
SAM Tools provide various utilities for manipulating alignments in the SAM format,
including sorting, merging, indexing and generating alignments in a per-position format. |
| scalapack |
numlib |
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
redesigned for distributed memory MIMD parallel computers. |
| sdl2 |
lib |
SDL: Simple DirectMedia Layer, a cross-platform multimedia library |
| snappy |
lib |
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. |
| soci |
lang |
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++. |
| sqlite |
devel |
SQLite: SQL Database Engine in a C Library |
| sratoolkit |
bio |
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 |
| szip |
tools |
Szip compression software, providing lossless compression of scientific data |
| tbb |
lib |
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. |
| tensorflow |
data |
TensorFlow is an open-source software library for Machine Intelligence.
|
| tesseract |
vis |
Tesseract is an optical character recognition engine |
| trimgalore |
bio |
Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. |
| trimmomatic |
bio |
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. |
| ucc |
lib |
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 |
lib |
Unified Communication X
An open-source production grade communication framework for data centric
and high-performance applications
|
| util-linux |
tools |
Set of Linux utilities |
| vcftools |
bio |
The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |
| x11 |
vis |
The X Window System (X11) is a windowing system for bitmap displays |
| x264 |
vis |
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 |
vis |
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.
|
| xorg-macros |
devel |
X.org macros utilities. |
| xz |
tools |
xz: XZ utilities |
| yaml-cpp |
tools |
yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec |
| yasm |
lang |
Yasm: Complete rewrite of the NASM assembler with BSD license |
| zlib |
lib |
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 |
lib |
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. |
