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

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.


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+
Build system: perl
Synopsis: Perl extension for Consistent Signal Handling
Description:
spades 4.2.0
Dependencies: bzip2@1.0.8 perl@5.36.0 python@3.11.14 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://ablab.github.io/spades/
Licenses: GPL 2
Build system: cmake
Synopsis: Genome assembly toolkit
Description:

SPAdes is an assembly toolkit containing various assembly pipelines.

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+
Build system: perl
Synopsis: Read/Write .css files with as little code as possible
Description:
metamaps 0.0-1.e23f8a8
Dependencies: boost@1.89.0 gsl@2.8 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/DiltheyLab/MetaMaps
Licenses: Public Domain
Build system: gnu
Synopsis: Long-read metagenomic analysis
Description:

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.

iq-tree 2.0.6
Dependencies: boost@1.89.0 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
Build system: cmake
Synopsis: Efficient software for phylogenomic inference
Description:

This package provides software for phylogenomic inference.

python-pycoqc 2.5.2
Propagated dependencies: python-h5py@3.13.0 python-jinja2@3.1.2 python-numpy@1.26.4 python-pandas@2.2.3 python-plotly@5.20.0 python-pysam@0.23.0 python-scipy@1.12.0 python-tqdm@4.67.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://a-slide.github.io/pycoQC/
Licenses: GPL 3
Build system: pyproject
Synopsis: QC plots for Nanopore basecallers
Description:

This package computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller.

r-nichenetr 2.0.4
Propagated dependencies: r-caret@7.0-1 r-catools@1.18.3 r-circlize@0.4.16 r-complexheatmap@2.26.0 r-cowplot@1.2.0 r-data-table@1.17.8 r-diagrammer@1.0.11 r-dicekriging@1.6.1 r-dplyr@1.1.4 r-e1071@1.7-16 r-emoa@0.5-3 r-fdrtool@1.2.18 r-ggforce@0.5.0 r-ggnewscale@0.5.2 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-hmisc@5.2-4 r-igraph@2.2.1 r-limma@3.66.0 r-magrittr@2.0.4 r-matrix@1.7-4 r-mlrmbo@1.1.5.1 r-parallelmap@1.5.1 r-purrr@1.2.0 r-randomforest@4.7-1.2 r-readr@2.1.6 r-rocr@1.0-11 r-seurat@5.3.1 r-shadowtext@0.1.6 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/saeyslab/nichenetr
Licenses: GPL 3
Build system: r
Synopsis: R implementation of the NicheNet method
Description:

The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

rsat 2022-06-26
Dependencies: perl@5.36.0 python@3.11.14 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+
Build system: gnu
Synopsis: Regulatory sequence analysis tools
Description:

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

python-nanomath 1.0.1
Propagated dependencies: python-deprecated@1.2.14 python-numpy@1.26.4 python-pandas@2.2.3
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/wdecoster/nanomath
Licenses: GPL 3
Build system: pyproject
Synopsis: Simple math function for other Oxford Nanopore scripts
Description:

This package contains a few simple math function for other Oxford Nanopore processing scripts.

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@2.6.1 perl@5.36.0 python@3.11.14 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@4.5.2 r-ggplot2@4.0.1 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
Build system: gnu
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.

cat 5.2.3
Dependencies: diamond@2.1.6 prodigal@2.6.3 python@3.11.14
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/dutilh/CAT
Licenses: Expat
Build system: gnu
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

perl-cgpvcf 2.0.4
Propagated dependencies: perl-bio-pipeline-comparison@1.123050 perl-const-fast@0.014 perl-data-uuid@1.226 perl-datetime@1.54
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://cancerit.github.io/cgpVcf/
Licenses: AGPL 3+
Build system: gnu
Synopsis: Set of common Perl utilities for generating VCF headers
Description:

This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.

assembly-stats 1.0.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/sanger-pathogens
Licenses: GPL 3
Build system: cmake
Synopsis: Tool to extract assembly statistics from FASTA and FASTQ files
Description:

This package provides a tool to extract assembly statistics from FASTA and FASTQ files.

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
Build system: cmake
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.

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+
Build system: perl
Synopsis: Generate syntax-hightlighted HTML for Perl using PPI
Description:
perl-bio-pipeline-comparison 1.123050
Dependencies: bioperl-minimal@1.7.0 perl-exception-class@1.44 perl-file-which@1.23 perl-moose@2.2015 perl-try-tiny@0.31
Propagated dependencies: htslib@1.21 which@2.21
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Bio-Pipeline-Comparison
Licenses: GPL 3+
Build system: perl
Synopsis: Comparative assesment of variant calling (CAVar)
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 perl-tidy@20250912
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+
Build system: perl
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.

primer3 2.6.1
Dependencies: perl@5.36.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://primer3.org/
Licenses: GPL 2
Build system: gnu
Synopsis: Tool to select primers for polymerase chain reaction
Description:

Primer3 is a widely used program for designing PCR primers. PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

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
Build system: gnu
Synopsis: Tool to view ICGC data
Description:

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

codemin 1.0.5
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/Illumina/strelka/tree/master/redist
Licenses: Expat
Build system: gnu
Synopsis: Set of lightweight minimization functions.
Description:

The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.

python-carputils 18.1-0.0b56f65
Propagated dependencies: python-numpy@1.26.4 python-ruamel.yaml@0.18.14 python-common@0.1.2 python-pydoe3@1.6.2 python-tables@3.10.2 python-scipy@1.12.0 python-matplotlib@3.8.2 python-pandas@2.2.3 python-six@1.17.0 python-dateutil@2.9.0
Channel: guix-science
Location: guix-science/packages/carputils.scm (guix-science packages carputils)
Home page: https://opencarp.org/about/opencarp-ecosystem#the-carputils-framework
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Python framework for access to openCARP
Description:

The carputils framework will be the optimal way to access openCARP for most users. This Python framework was developed to provide the means to easily encode in silico experiments including pre- and postprocessing. carputils will call the openCARP simulator.

python-common 0.1.2
Channel: guix-science
Location: guix-science/packages/carputils.scm (guix-science packages carputils)
Home page: https://pypi.org/project/common
Licenses: Expat
Build system: pyproject
Synopsis: Common tools and data structures implemented in pure Python
Description:

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

python-pydoe3 1.6.2
Propagated dependencies: python-numpy@1.26.4 python-scipy@1.12.0
Channel: guix-science
Location: guix-science/packages/carputils.scm (guix-science packages carputils)
Home page: https://github.com/relf/pyDOE3
Licenses: Modified BSD
Build system: pyproject
Synopsis: Design of experiments for Python
Description:

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

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Total results: 68658