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| align="center" | [https://arrow.apache.org arrow] | | align="center" | [https://arrow.apache.org arrow] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 0.11.1, 0.15.1, 0.16.0, 0.17.1 | | align="center" | 0.11.1, 0.15.1, 0.16.0, 0.17.1, 2.0.0, 5.0.0, 7.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div> | ||
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| align="center" | - | | align="center" | - | ||
| align="center" | 1.03 | | align="center" | 1.03 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage: https://sites.google.com/site/bgcsoftware/<br /><br /><br /></div> | ||
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| align="center" | [https://bitbucket.org/gavinband/bgen/src/default/ bgen] | | align="center" | [https://bitbucket.org/gavinband/bgen/src/default/ bgen] | ||
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| align="center" | phys | | align="center" | phys | ||
| align="center" | 1.2.5 | | align="center" | 1.2.5 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage: http://www.icams.de/content/departments/cmat/boltztrap/ Keyword:phys<br /><br /><br /></div> | ||
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| align="center" | [https://www.boost.org/ boost] | | align="center" | [https://www.boost.org/ boost] | ||
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| align="center" | 1.31.0 | | align="center" | 1.31.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: https://chapel-lang.org URL: https://chapel-lang.org<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: https://chapel-lang.org URL: https://chapel-lang.org<br /><br /><br /></div> | ||
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| align="center" | [https://github.com/simnibs/charm-gems charm-gems] | |||
| align="center" | - | |||
| align="center" | 1.3.3 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This repository contains the gems C++ code and python bindings used in Freesurfer's Sequence-Adaptive Multimodal SEGmentation (SAMSEG) and in SimNIBS 4.0 Complete Head Anatomy Reconstruction Method (CHARM) to create individualized head models for electric field simulations. Homepage: https://github.com/simnibs/charm-gems URL: https://github.com/simnibs/charm-gems Compatible modules: python/3.11, python/3.10 Extensions: charm-gems-1.3.3<br /><br /><br /></div> | |||
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| align="center" | [https://github.com/SebWouters/CheMPS2 chemps2] | | align="center" | [https://github.com/SebWouters/CheMPS2 chemps2] | ||
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| align="center" | [https://fmm3d.readthedocs.io fmm3d] | | align="center" | [https://fmm3d.readthedocs.io fmm3d] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 1.0.1 | | align="center" | 1.0.1, 1.0.4 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine. Homepage: https://fmm3d.readthedocs.io URL: https://fmm3d.readthedocs.io Compatible modules: python/3. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine. Homepage: https://fmm3d.readthedocs.io URL: https://fmm3d.readthedocs.io Compatible modules: python/3.11, python/3.10<br /><br /><br /></div> | ||
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| align="center" | [https://fmriprep.org/ fmriprep] | | align="center" | [https://fmriprep.org/ fmriprep] | ||
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| align="center" | [https://github.com/ekg/fsom fsom] | | align="center" | [https://github.com/ekg/fsom fsom] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 20141119 | | align="center" | 20141119, 20151117 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tiny C library for managing SOM (Self-Organizing Maps) neural networks. Homepage: https://github.com/ekg/fsom URL: https://github.com/ekg/fsom<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tiny C library for managing SOM (Self-Organizing Maps) neural networks. Homepage: https://github.com/ekg/fsom URL: https://github.com/ekg/fsom<br /><br /><br /></div> | ||
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| align="center" | vis | | align="center" | vis | ||
| align="center" | 5.99.0 | | align="center" | 5.99.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace Keyword:vis<br /><br /><br /></div> | ||
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| align="center" | [http://grackle.readthedocs.io grackle] | | align="center" | [http://grackle.readthedocs.io grackle] | ||
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| align="center" | math | | align="center" | math | ||
| align="center" | 4.0.3, 5.1.0 | | align="center" | 4.0.3, 5.1.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math<br /><br /><br /></div> | ||
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| align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis-64idx] | | align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis-64idx] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.0.1 | | align="center" | 2.0.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. Homepage: http://genome.sph.umich.edu/wiki/Minimac3 Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://genome.sph.umich.edu/wiki/Minimac4 minimac4] | | align="center" | [https://genome.sph.umich.edu/wiki/Minimac4 minimac4] | ||
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| align="center" | 2.0.13 | | align="center" | 2.0.13 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NGT provides commands and a library for performing high-speed approximate nearest neighbor searches against a large volume of data in high dimensional vector data space (several ten to several thousand dimensions). Homepage: https://github.com/yahoojapan/NGT URL: https://github.com/yahoojapan/NGT Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: ngt-2.0.13<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NGT provides commands and a library for performing high-speed approximate nearest neighbor searches against a large volume of data in high dimensional vector data space (several ten to several thousand dimensions). Homepage: https://github.com/yahoojapan/NGT URL: https://github.com/yahoojapan/NGT Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: ngt-2.0.13<br /><br /><br /></div> | ||
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| align="center" | [https://nipy.github.io/nibabel nibabel] | |||
| align="center" | - | |||
| align="center" | 5.2.0 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. Homepage: https://nipy.github.io/nibabel URL: https://nipy.github.io/nibabel Compatible modules: python/3.10, python/3.11 Extensions: bz2file-0.98, nibabel-5.2.0, pydicom-2.4.4<br /><br /><br /></div> | |||
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| align="center" | [https://ninja-build.org/ ninja] | | align="center" | [https://ninja-build.org/ ninja] | ||
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| align="center" | 10.31, 10.34 | | align="center" | 10.31, 10.34 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/<br /><br /><br /></div> | ||
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| align="center" | [https://pdal.io/ pdal] | |||
| align="center" | - | |||
| align="center" | 2.7.1 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PDAL is Point Data Abstraction Library. It is a C/C++ open source library and applications for translating and processing point cloud data. It is not limited to LiDAR data, although the focus and impetus for many of the tools in the library have their origins in LiDAR. Homepage: https://pdal.io/ URL: https://pdal.io/<br /><br /><br /></div> | |||
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| align="center" | [https://www.cs.uoregon.edu/research/pdt/ pdt] | | align="center" | [https://www.cs.uoregon.edu/research/pdt/ pdt] | ||
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| align="center" | geo | | align="center" | geo | ||
| align="center" | 1.0 | | align="center" | 1.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran Keyword:geo<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran URL: https://github.com/mhagdorn/proj4-fortran Keyword:geo<br /><br /><br /></div> | ||
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| align="center" | [https://www.vicbioinformatics.com/software.prokka.shtml prokka] | | align="center" | [https://www.vicbioinformatics.com/software.prokka.shtml prokka] | ||
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| align="center" | 1.5.3 | | align="center" | 1.5.3 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Homepage: https://gatb.inria.fr/software/simka/ URL: https://gatb.inria.fr/software/simka/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Homepage: https://gatb.inria.fr/software/simka/ URL: https://gatb.inria.fr/software/simka/<br /><br /><br /></div> | ||
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| align="center" | [https://simnibs.github.io/simnibs simnibs] | |||
| align="center" | - | |||
| align="center" | 4.1.0 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation Homepage: https://simnibs.github.io/simnibs URL: https://simnibs.github.io/simnibs Compatible modules: python/3.11, python/3.10 Extensions: msgpack-1.0.7, PyOpenGL-3.1.7, PyOpenGL-accelerate-3.1.7, SimNIBS-4.1.0<br /><br /><br /></div> | |||
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| align="center" | [https://github.com/precimed/simu simu] | | align="center" | [https://github.com/precimed/simu simu] | ||
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| align="center" | [https://github.com/ekg/tabixpp tabixpp] | | align="center" | [https://github.com/ekg/tabixpp tabixpp] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 1.1.0 | | align="center" | 1.1.0, 1.1.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C++ wrapper to tabix indexer Homepage: https://github.com/ekg/tabixpp URL: https://github.com/ekg/tabixpp<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C++ wrapper to tabix indexer Homepage: https://github.com/ekg/tabixpp URL: https://github.com/ekg/tabixpp<br /><br /><br /></div> | ||
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| align="center" | [https://github.com/vcflib/vcflib vcflib] | | align="center" | [https://github.com/vcflib/vcflib vcflib] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 1.0.1, 1.0.3 | | align="center" | 1.0.1, 1.0.3, 1.0.9 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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. Homepage: https://github.com/vcflib/vcflib URL: https://github.com/vcflib/vcflib<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 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. Homepage: https://github.com/vcflib/vcflib URL: https://github.com/vcflib/vcflib<br /><br /><br /></div> | ||
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| align="center" | 3.1.4, 4.0.3, 4.2.0 | | align="center" | 3.1.4, 4.0.3, 4.2.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. Homepage: https://code.ornl.gov/neams-workbench/wasp URL: https://code.ornl.gov/neams-workbench/wasp<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. Homepage: https://code.ornl.gov/neams-workbench/wasp URL: https://code.ornl.gov/neams-workbench/wasp<br /><br /><br /></div> | ||
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| align="center" | [https://github.com/smarco/WFA2-lib wfa2] | |||
| align="center" | - | |||
| align="center" | 2.3.4 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. Homepage: https://github.com/smarco/WFA2-lib URL: https://github.com/smarco/WFA2-lib<br /><br /><br /></div> | |||
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| align="center" | [http://www.cpc.noaa.gov/products/wesley/wgrib2/ wgrib2] | | align="center" | [http://www.cpc.noaa.gov/products/wesley/wgrib2/ wgrib2] | ||