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

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.


allelecount 4.2.1
Dependencies: zlib@1.3.1 htslib@1.21 perl-pod-coverage@0.23 perl-file-which@1.23 perl-test-fatal@0.016 perl-try-tiny@0.31 samtools@1.19
Propagated dependencies: perl-const-fast@0.014 perl-sub-exporter-progressive@0.001013 perl-bio-db-hts@3.01 bioperl-minimal@1.7.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/cancerit/alleleCount
Licenses: AGPL 3+
Build system: gnu
Synopsis: Support code for NGS copy number algorithms
Description:

This package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenburg.

booster 0.1.2-0.b9eee32
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://booster.c3bi.pasteur.fr/
Licenses: GPL 2
Build system: gnu
Synopsis: BOOtstrap Support by TransfER
Description:

This package provides a new way of computing bootstrap supports in large phylogenies.

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.

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.

iqtree3 3.0.1
Dependencies: boost@1.89.0 eigen@3.4.0 yaml-cpp@0.8.0-0.2f86d13 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://iqtree.github.io/
Licenses: GPL 2
Build system: cmake
Synopsis: Efficient and versatile phylogenomic inference (version 3)
Description:

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.

As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.

Key features of IQ-TREE:

  • Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood;

  • An ultrafast bootstrap approximation (UFBoot) to assess branch supports;

  • An ultrafast and automatic model selection (ModelFinder);

  • A flexible simulator (AliSim) which can simulate sequence alignments under more realistic models than Seq-Gen and INDELible;

  • Several fast branch tests like SH-aLRT and aBayes test and tree topology tests like the approximately unbiased (AU) test.

This package provides IQ-TREE version 3.

python-nanoget 1.19.4
Propagated dependencies: python-biopython@1.85 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/wdecoster/nanoget
Licenses: GPL 3
Build system: pyproject
Synopsis: Functions for Oxford Nanopore sequencing data and alignments
Description:

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.

pcap-core 3.5.0
Propagated dependencies: bwa@0.7.18 samtools@1.19 biobambam@0.0.191
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/ICGC-TCGA-PanCancer/PCAP-core
Licenses: GPL 2+
Build system: gnu
Synopsis: NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project
Description:
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.

python-primer3-py 2.2.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://libnano.github.io/primer3-py/
Licenses: GPL 2
Build system: pyproject
Synopsis: Simple oligo analysis and primer design
Description:

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

perl-set-intervaltree 0.10
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Set-IntervalTree
Licenses: GPL 1+
Build system: perl
Synopsis: Perform range-based lookups on sets of ranges.
Description:
cat-pack 6.0.1
Dependencies: bash-minimal@5.2.37 bwa@0.7.18 diamond@2.1.6 mmseqs2@18 prodigal@2.6.3 python@3.11.14 samtools@1.19
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/MGXlab/CAT_pack
Licenses: Expat
Build system: gnu
Synopsis: Tool for taxonomic classification of contigs and metagenome-assembled genomes
Description:

CAT and BAT are pipelines for the taxonomic classification of long DNA sequences and MAGs 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.

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
Build system: gnu
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.

lsd2 2.4.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://iqtree.github.io/
Licenses: GPL 2
Build system: cmake
Synopsis: Fast dating using least-squares criteria and algorithms
Description:

This package provides a phylogeny dating method using least-squares algorithms and criteria.

hiddendomains 3.1
Dependencies: perl@5.36.0
Propagated dependencies: r-depmixs4@1.5-1 r-hiddenmarkov@1.8-14
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://hiddendomains.sourceforge.net
Licenses: GPL 2
Build system: gnu
Synopsis: Programs used to identify enrichment of ChIP-seq reads
Description:

hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.

sharc 1.0-slurm
Dependencies: gawk@5.3.0 bash@5.2.37 coreutils@9.1 emboss@6.5.7 grep@3.11 qsub-slurm@0.0.7 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 6.0.1
Dependencies: bash-minimal@5.2.37 bwa@0.7.18 diamond@2.1.6 mmseqs2@18 prodigal@2.6.3 python@3.11.14 samtools@1.19
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/MGXlab/CAT_pack
Licenses: Expat
Build system: gnu
Synopsis: Tool for taxonomic classification of contigs and metagenome-assembled genomes
Description:

CAT and BAT are pipelines for the taxonomic classification of long DNA sequences and MAGs 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.

iqtree2 2.4.0
Dependencies: boost@1.89.0 eigen@3.4.0 yaml-cpp@0.8.0-0.2f86d13 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://iqtree.github.io/
Licenses: GPL 2
Build system: cmake
Synopsis: Efficient and versatile phylogenomic inference (version 2)
Description:

The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.

As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.

Key features of IQ-TREE:

  • Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood;

  • An ultrafast bootstrap approximation (UFBoot) to assess branch supports;

  • An ultrafast and automatic model selection (ModelFinder);

  • A flexible simulator (AliSim) which can simulate sequence alignments under more realistic models than Seq-Gen and INDELible;

  • Several fast branch tests like SH-aLRT and aBayes test and tree topology tests like the approximately unbiased (AU) test.

This package provides IQ-TREE version 2.

python-pydeseq2 0.5.4
Propagated dependencies: python-anndata@0.11.4 python-formulaic@1.0.1 python-formulaic-contrasts@1.0.0 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/owkin/PyDESeq2
Licenses: Expat
Build system: pyproject
Synopsis: Python implementation of DESeq2
Description:

This package provides a python implementation of DESeq2.

python-nanofilt 2.8.0
Propagated dependencies: python-biopython@1.85 python-pandas@2.2.3
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/wdecoster/nanofilt
Licenses: GPL 3
Build system: pyproject
Synopsis: Filtering and trimming of Oxford Nanopore Sequencing data
Description:

This package provides tools for filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. It is intended to be used directly after fastq extraction, prior to mapping, or in a stream between extraction and mapping.

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.

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-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.

blt 0.7.1
Channel: guix-science
Location: guix-science/packages/cmake.scm (guix-science packages cmake)
Home page: https://llnl-blt.readthedocs.io/en/develop/
Licenses: Modified BSD
Build system: copy
Synopsis: CMake macros and tools aimed at HPC software development
Description:

BLT is a streamlined CMake-based foundation for Building, Linking and Testing large-scale high performance computing (HPC) application.

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Total results: 69112