_            _    _        _         _
      /\ \         /\ \ /\ \     /\_\      / /\
      \_\ \       /  \ \\ \ \   / / /     / /  \
      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
  / / /      / / /   / / /   \ \ \   _    \ \ \
 / / /      / / /___/ / /     \ \ \ /_/\__/ / /
/_/ /      / / /____\/ /       \ \_\\ \/___/ /
\_\/       \/_________/         \/_/ \_____\/

Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.

API method:

GET /api/packages?search=hello&page=1&limit=20

where search is your query, page is a page number and limit is a number of items on a single page. Pagination information (such as a number of pages and etc) is returned in response headers.

If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


rsat 2022-06-26
Dependencies: perl@5.36.0 python@3.11.11 python-pyyaml@6.0.2
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://rsat.france-bioinformatique.fr/teaching/RSAT_portal.html
Licenses: AGPL 3+
Synopsis: Regulatory sequence analysis tools
Description:

This package provides a subset of the Regulatory Sequence Analysis Tools (RSAT).

python-mellon 1.6.1
Propagated dependencies: python-jax@0.4.28 python-jaxopt@0.8.3 python-pynndescent@0.5.13 python-scikit-learn@1.7.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/settylab/mellon
Licenses: GPL 3
Synopsis: Non-parametric cell-state density estimator
Description:

Mellon is a non-parametric cell-state density estimator based on a nearest-neighbors-distance distribution. It uses a sparse gaussian process to produce a differntiable density function that can be evaluated out of sample.

perl-sys-sigaction 0.23
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Sys-SigAction
Licenses: GPL 1+
Synopsis: Perl extension for Consistent Signal Handling
Description:
sharc 1.0-local
Dependencies: gawk@5.3.0 bash@5.2.37 coreutils@9.1 emboss@6.5.7 grep@3.11 qsub-local@0.0.1 minimap2@2.28 primer3@1.1.4 perl@5.36.0 python@3.11.11 python-aniso8601@10.0.1 python-certifi@2025.06.15 python-chardet@5.2.0 python-configparser@7.2.0 python-flask@3.1.0 python-flask-restful@0.3.10 python-idna@3.10 python-itsdangerous@2.2.0 python-jinja2@3.1.2 python-markupsafe@3.0.2 nanosv@1.2.4 python-pymongo@4.14.0 python-pysam@0.23.0 python-pytz@2025.1 python-pyvcf3@1.0.3-0.1fb3789 python-requests@2.32.5 python-six@1.17.0 python-urllib3@2.5.0 python-werkzeug@3.1.3 python2@2.7.18 r-minimal@4.5.0 r-ggplot2@3.5.2 r-randomforest@4.7-1.2 r-rocr@1.0-11 sambamba@0.8.2 sed@4.9 gnomad-sv-sites@2.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/UMCUGenetics/SHARC
Licenses: GPL 3
Synopsis: Somatic SV pipeline for tumor-only Nanopore sequencing data
Description:

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

fastqc 0.11.9
Propagated dependencies: perl@5.36.0 icedtea@2.6.13
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Licenses: GPL 3+ ASL 2.0
Synopsis: A quality control tool for high throughput sequence data
Description:

FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.

python-formulaic-contrasts 1.0.0
Propagated dependencies: python-formulaic@1.0.1 python-pandas@2.2.3 python-session-info@1.0.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/scverse/formulaic-contrasts
Licenses: Modified BSD
Synopsis: Build contrasts for models defined with formulaic
Description:

Build contrasts for models defined with formulaic.

perl-ppi-html 1.08
Dependencies: perl-css-tiny@1.20 perl-params-util@1.102 perl-ppi@1.277
Propagated dependencies: perl-module-install@1.19
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/PPI-HTML
Licenses: GPL 1+
Synopsis: Generate syntax-hightlighted HTML for Perl using PPI
Description:
seqan 3.0.2
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Synopsis: Library for nucleotide sequence analysis
Description:

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

fastq-tools 0.8.3
Dependencies: pcre@8.45 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://homes.cs.washington.edu/~dcjones/fastq-tools/
Licenses: Expat
Synopsis: Tools to work with FASTQ files
Description:

This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

score-client 5.0.0
Dependencies: openjdk@11.0.22
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://docs.icgc.org/software/download/#score-client
Licenses: GPL 3
Synopsis: Tool to view ICGC data
Description:

This package provides a tool to download or view data in the cloud environments of ICGC.

perl-findbin-libs 2.15
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/FindBin-libs
Licenses: GPL 1+
Synopsis:
Description:
sharc 1.0-sge
Dependencies: gawk@5.3.0 bash@5.2.37 coreutils@9.1 emboss@6.5.7 grep@3.11 grid-engine-core@8.1.9 minimap2@2.28 primer3@1.1.4 perl@5.36.0 python@3.11.11 python-aniso8601@10.0.1 python-certifi@2025.06.15 python-chardet@5.2.0 python-configparser@7.2.0 python-flask@3.1.0 python-flask-restful@0.3.10 python-idna@3.10 python-itsdangerous@2.2.0 python-jinja2@3.1.2 python-markupsafe@3.0.2 nanosv@1.2.4 python-pymongo@4.14.0 python-pysam@0.23.0 python-pytz@2025.1 python-pyvcf3@1.0.3-0.1fb3789 python-requests@2.32.5 python-six@1.17.0 python-urllib3@2.5.0 python-werkzeug@3.1.3 python2@2.7.18 r-minimal@4.5.0 r-ggplot2@3.5.2 r-randomforest@4.7-1.2 r-rocr@1.0-11 sambamba@0.8.2 sed@4.9 gnomad-sv-sites@2.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/UMCUGenetics/SHARC
Licenses: GPL 3
Synopsis: Somatic SV pipeline for tumor-only Nanopore sequencing data
Description:

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

cgp-cavemanwrapper 1.16.0
Propagated dependencies: perl-file-path@2.16 perl-file-which@1.23 perl-const-fast@0.014 perl-capture-tiny@0.48 perl-ipc-system-simple@1.26 perl-try-tiny@0.31 perl-carp@1.50 perl-forks@0.36 pcap-core@3.5.0 perl@5.36.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/cancerit/cgpCaVEManWrapper
Licenses: AGPL 3+
Synopsis: Reference implementation of CGP workflow for CaVEMan
Description:

This package provides the reference implementation of CGP workflow for CaVEMan SNV analysis.

cat 5.2.3
Dependencies: diamond@2.1.6 prodigal@2.6.3 python@3.11.11
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/dutilh/CAT
Licenses: Expat
Synopsis: Tool for taxonomic classification of contigs and metagenome-assembled genomes
Description:

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately

star-fusion 1.0.0
Dependencies: perl@5.36.0 samtools@1.19 coreutils@9.1 gzip@1.14
Propagated dependencies: perl-carp@1.50 perl-pathtools@3.75 perl-db-file@1.858 perl-uri@5.05 perl-set-intervaltree@0.10
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/STAR-Fusion/STAR-Fusion/
Licenses: Modified BSD
Synopsis: Fusion detection based on STAR
Description:

This package provides a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). It uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. It further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

last 1080
Dependencies: zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://last.cbrc.jp/
Licenses: GPL 3
Synopsis: Genome-scale sequence comparison
Description:
biobambam 0.0.191
Dependencies: libmaus@0.0.196 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/gt1/biobambam
Licenses: GPL 3+
Synopsis: Collection of tools to work with BAM files
Description:

This package contains the following programs: bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq.

perl-acme-damn 0.08
Dependencies: perl-test-exception@0.43
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Acme-Damn
Licenses: GPL 1+
Synopsis: 'Unbless' Perl objects.
Description:
igv 2.16.2
Propagated dependencies: openjdk@11.0.22
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://www.broadinstitute.org/software/igv/
Licenses: Expat
Synopsis: Integrative Genomics Viewer
Description:

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

perl-css-tiny 1.20
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/CSS-Tiny
Licenses: GPL 1+
Synopsis: Read/Write .css files with as little code as possible
Description:
perl-devel-cover 1.40
Propagated dependencies: perl-browser-open@0.04 perl-capture-tiny@0.48 perl-class-xsaccessor@1.19 perl-moo@1.007000 perl-namespace-clean@0.27 perl-parallel-iterator@1.00 perl-pod-coverage@0.23 perl-ppi-html@1.08 perl-template-toolkit@2.28 perl-test-differences@0.67 perltidy@20180220
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Devel-Cover
Licenses: GPL 1+
Synopsis: Code coverage metrics for Perl
Description:

This module provides code coverage metrics for Perl. Code coverage metrics describe how thoroughly tests exercise code. By using Devel::Cover you can discover areas of code not exercised by your tests and determine which tests to create to increase coverage.

iq-tree 2.0.6
Dependencies: boost@1.83.0 eigen@3.4.0 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://www.iqtree.org/
Licenses: GPL 2
Synopsis: Efficient software for phylogenomic inference
Description:

This package provides software for phylogenomic inference.

perl-ppi 1.277
Dependencies: perl-clone@0.43 perl-io-string@1.08 perl-list-moreutils@0.430 perl-params-util@1.102 perl-task-weaken@1.06
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/PPI
Licenses: GPL 1+
Synopsis: Parse, Analyze and Manipulate Perl (without perl)
Description:
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