Toys / Webring for GNU Guix channels

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.

cgp-pindel 2.2.4

Propagated dependencies: perl@5.36.0 pcap-core@3.5.0 perl-cgpvcf@2.0.4 bioperl-minimal@1.7.0 perl-bio-db-hts@3.01 perl-const-fast@0.014 perl-file-which@1.23 perl-pod-coverage@0.23 perl-list-moreutils@0.430 perl-test-fatal@0.016 perl-try-tiny@0.31 perl-capture-tiny@0.48 perl-term-ui@0.50 perl-log-message@0.08 perl-ipc-system-simple@1.26 perl-sub-exporter-progressive@0.001013 perl-devel-cover@1.40

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/cancerit/cgpPindel

Licenses: AGPL 3+

Build system: gnu

Synopsis: Cancer Genome Projects workflow for Pindel.

Description:

cgp-cavemanpostprocessing 1.8.9

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 perl-attribute-util@1.07 perl-config-inifiles@3.000002 perl-set-intervaltree@0.10 perl-libwww@6.78 pcap-core@3.5.0 perl-cgpvcf@2.0.4 perl-bio-db-hts@3.01 bioperl-minimal@1.7.0 perl@5.36.0

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/cancerit/cgpCaVEManPostProcessing

Licenses: AGPL 3+

Build system: gnu

Synopsis: Flagging add-on to CaVEMan

Description:

This package is used to apply filtering on raw VCF calls generated using CaVEMan.

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.

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@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.

star 2.4.2a

Dependencies: htslib@1.21 zlib@1.3.1

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/alexdobin/STAR

Licenses: GPL 3+

Build system: gnu

Synopsis: Universal RNA-seq aligner

Description:

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

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+

Build system: perl

Synopsis:

Description:

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.

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.

perl-term-ui 0.50

Propagated dependencies: perl-log-message-simple@0.10

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: http://search.cpan.org/dist/Term-UI

Licenses: GPL 1+

Build system: perl

Synopsis: User interfaces via Term::ReadLine made easy

Description:

r-rblast 0.99.4-1.2319817

Dependencies: blast+@2.17.0

Propagated dependencies: r-biostrings@2.78.0

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/mhahsler/rBLAST

Licenses: GPL 3

Build system: r

Synopsis: R Interface for the Basic Local Alignment Search Tool

Description:

This package provides an interface for the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This includes interfaces to blastn, blastp, blastx, and makeblastdb.

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

Build system: pyproject

Synopsis: Build contrasts for models defined with formulaic

Description:

Build contrasts for models defined with formulaic.

r-scriabin 0.0.0.9000-1.313d15e

Propagated dependencies: r-ade4@1.7-23 r-cellid@1.18.0 r-circlize@0.4.16 r-clipr@0.8.0 r-complexheatmap@2.26.0 r-complexheatmap@2.26.0 r-cowplot@1.2.0 r-dplyr@1.1.4 r-factoextra@1.0.7 r-fsa@0.10.0 r-genefilter@1.92.0 r-ggalluvial@0.12.5 r-ggfittext@0.10.2 r-ggplot2@4.0.1 r-ggsci@4.1.0 r-limma@3.66.0 r-magrittr@2.0.4 r-matrix@1.7-4 r-matrixstats@1.5.0 r-networkd3@0.4.1 r-nichenetr@2.0.4 r-pbapply@1.7-4 r-qlcmatrix@0.9.9 r-scales@1.4.0 r-scater@1.38.0 r-seurat@5.3.1 r-tibble@3.3.0 r-tidyft@0.9.20 r-wgcna@1.73

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/BlishLab/scriabin

Licenses: Expat

Build system: r

Synopsis: Single-cell resolved interaction analysis through binning

Description:

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.

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:

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

Build system: gnu

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+

Build system: gnu

Synopsis: Collection of tools to work with BAM files

Description:

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

easel 0.49

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: http://bioeasel.org/

Licenses: FreeBSD

Build system: gnu

Synopsis: Sequence analysis library from The Eddy/Rivas Laboratory

Description:

Easel is an ANSI C code library developed by the Eddy/Rivas laboratory at Harvard. Easel supports our work on computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions.

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.

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.

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:

perl-prokka 1.14.6

Dependencies: aragorn@1.2.41 bioperl-minimal@1.7.0 blast+@2.17.0 findutils@4.10.0 hmmer@3.3.2 infernal@1.1.4 minced@0.3.2 parallel@20251122 perl@5.36.0 perl-data-dumper@2.183 perl-digest-md5@2.58 perl-findbin-libs@2.15 perl-module-build@0.4231 perl-scalar-list-utils@1.62 perl-time-piece@1.3401 perl-xml-simple@2.25 prodigal@2.6.3

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/tseemann/prokka

Licenses: GPL 3

Build system: gnu

Synopsis: Rapid prokaryotic genome annotation

Description:

This package provides tools for rapid prokaryotic genome annotation.

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.

libmaus 0.0.196

Dependencies: zlib@1.3.1

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/gt1/libmaus

Licenses: GPL 3+

Build system: gnu

Synopsis: Collection of bioinformatics data structures and algorithms

Description:

This package contains a collection of bioinformatics data structures and algorithms. It provides I/O classes, bitio classes, text indexing classes and BAM sequence alignment functionality.

python-nanostat 1.4.0

Propagated dependencies: python-nanoget@1.19.4 python-nanomath@1.0.1

Channel: guix-science

Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)

Home page: https://github.com/wdecoster/nanostat

Licenses: GPL 3

Build system: pyproject

Synopsis: Statistics for Oxford Nanopore sequencing data and alignments

Description:

This package provides procedures to calculate statistics for Oxford Nanopore sequencing data and alignments.

perl-css-tiny 1.20

Channel: guix-science