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

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.


python-hicmatrix 17.1
Dependencies: c-blosc2@2.15.2
Propagated dependencies: python-cooler@0.9.3 python-intervaltree@3.1.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scipy@1.12.0 python-tables@3.10.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/deeptools/HiCMatrix/
Licenses: GPL 3+
Build system: pyproject
Synopsis: HiCMatrix class for HiCExplorer and pyGenomeTracks
Description:

This helper package implements the HiCMatrix class for the HiCExplorer and pyGenomeTracks packages.

jellyfish 2.3.0
Dependencies: htslib@1.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://www.genome.umd.edu/jellyfish.html
Licenses: GPL 3+ Modified BSD
Build system: gnu
Synopsis: Tool for fast counting of k-mers in DNA
Description:

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the jellyfish dump command, or queried for specific k-mers with jellyfish query.

salmon 1.10.3
Dependencies: boost@1.83.0 bzip2@1.0.8 cereal@1.3.2 curl@8.6.0 eigen@3.4.0 htscodecs@1.6.1 jemalloc@5.3.0 libgff@2.0.0 tbb@2021.6.0 libstadenio@1.14.8 xz@5.4.5 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/COMBINE-lab/salmon
Licenses: GPL 3+
Build system: cmake
Synopsis: Quantification from RNA-seq reads using lightweight alignments
Description:

Salmon is a program to produce highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference.

ngshmmalign 0.1.1
Dependencies: boost@1.89.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cbg-ethz/ngshmmalign/
Licenses: GPL 2+
Build system: cmake
Synopsis: Profile HMM aligner for NGS reads
Description:

ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and HCV) that experience substantial biological insertions and deletions.

r-codeandroll2 2.3.6-1.d58e258
Propagated dependencies: r-colorramps@2.3.4 r-dplyr@1.1.4 r-gplots@3.2.0 r-gtools@3.9.5 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-sessioninfo@1.2.3 r-sm@2.2-6.0 r-stringendo@0.6.0-1.15594b1 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/CodeAndRoll2
Licenses: GPL 3
Build system: r
Synopsis: CodeAndRoll2 for vector, matrix and list manipulations
Description:

CodeAndRoll2 is a set of more than 130 productivity functions. These functions are used by MarkdownReports, ggExpress, and SeuratUtils.

r-illuminahumanmethylationepicmanifest 1.0.0-1.a9ffbad
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Human Methylation Manifest 1.0 B5 for R and minfi
Description:

This is a drop-in replacement for the IlluminaHumanMethylationEPIC package. It utilizes a Manifest based on 1.0B5 annotation. As of version 0.3.0, the IlluminaHumanMethylationEPIC package still employs the 1.0B2 annotation manifest. A corresponding annotation package, IlluminaHumanMethylationEPICanno.ilm10b5.hg38, is available to ensure proper annotation. The decision to maintain the same name is due to complications in downstream processing caused by array name lookup in certain preprocessing options.

r-plsdabatch 0.2.3-1.4aadf3a
Propagated dependencies: r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-gridextra@2.3 r-lmertest@3.1-3 r-mixomics@6.34.0 r-mvtnorm@1.3-3 r-performance@0.15.2 r-rdpack@2.6.4 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/EvaYiwenWang/PLSDAbatch
Licenses: GPL 3
Build system: r
Synopsis: PLSDA-batch
Description:

This package provides a new batch effect correction method based on Projection to Latent Structures Discriminant Analysis named “PLSDA-batch” to correct data prior to any downstream analysis. PLSDA-batch estimates latent components related to treatment and batch effects to remove batch variation. The method is multivariate, non-parametric and performs dimension reduction. Combined with centered log ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far.

python-genomic-regions 0.0.10
Propagated dependencies: python-future@1.0.0 python-intervaltree@3.1.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pybedtools@0.10.0 python-pybigwig@0.3.22 python-pytest@8.4.1 python-msgpack-numpy@0.4.8 python-cython@3.1.2 python-msgpack@1.1.1 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pypi.org/project/genomic-regions/
Licenses: Expat
Build system: pyproject
Synopsis: Consistently handle genomic regions
Description:

This package aims to simplify working with genomic region / interval data by providing a common interface that lets you access a wide selection of file types and formats for handling genomic region data---all using the same syntax.

seqan 2.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Build system: trivial
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.

python-cyvcf2 0.31.2
Dependencies: curl@8.6.0 htslib@1.21 libdeflate@1.19 openssl@3.0.8 zlib@1.3.1
Propagated dependencies: python-click@8.1.8 python-coloredlogs@10.0 python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/brentp/cyvcf2/
Licenses: Expat
Build system: pyproject
Synopsis: Fast vcf file parsing with Cython and htslib
Description:

Cyvcf2 is a Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

taxtastic 0.11.1
Propagated dependencies: python-biopython@1.85 python-decorator@5.2.1 python-dendropy@4.5.1 python-fastalite@0.4.1 python-jinja2@3.1.2 python-pandas@2.2.3 python-psycopg@3.2.4 python-psycopg2-binary@2.9.10 python-pyyaml@6.0.2 python-sqlalchemy@2.0.36 python-sqlparse@0.5.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/fhcrc/taxtastic
Licenses: GPL 3+
Build system: pyproject
Synopsis: Tools for taxonomic naming and annotation
Description:

Taxtastic is software written in python used to build and maintain reference packages i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.

python-cmseq 1.0.4
Dependencies: samtools@1.19
Propagated dependencies: python-bcbio-gff@0.6.9 python-biopython@1.73 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/SegataLab/cmseq/
Licenses: Expat
Build system: pyproject
Synopsis: Set of utilities on sequences and BAM files
Description:

CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus.

filtlong 0.2.0-1.d1bb46d
Dependencies: bash-minimal@5.2.37 gawk@5.3.0 python-wrapper@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rrwick/Filtlong/
Licenses: GPL 3 ASL 2.0
Build system: gnu
Synopsis: Tool for quality filtering of Nanopore and PacBio data
Description:

The Filtlong package is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

r-seuratextend 1.2.5-1.5dacd7c
Propagated dependencies: r-biocmanager@1.30.27 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-glue@1.8.0 r-hdf5r@1.3.12 r-magrittr@2.0.4 r-mosaic@1.9.2 r-purrr@1.2.0 r-remotes@2.5.0 r-reshape2@1.4.5 r-reticulate@1.44.1 r-rlist@0.4.6.2 r-scales@1.4.0 r-seurat@5.3.1 r-seuratextenddata@0.2.1-1.e7f17d4 r-seuratobject@5.2.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huayc09/SeuratExtend
Licenses: GPL 3+
Build system: r
Synopsis: Enhanced toolkit for scRNA-seq analysis
Description:

This package is designed to improve and simplify the analysis of scRNA-seq data. It uses the Seurat object for this purpose. It provides an array of enhanced visualization tools, an integrated functional and pathway analysis pipeline, seamless integration with popular Python tools, and a suite of utility functions to aid in data manipulation and presentation.

sortmerna 4.3.7
Dependencies: concurrentqueue@1.0.3 gflags@2.2.2 rapidjson@1.1.0-1.949c771 rocksdb@10.4.2 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinfo.lifl.fr/RNA/sortmerna/
Licenses: LGPL 3
Build system: cmake
Synopsis: Biological sequence analysis tool for NGS reads
Description:

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU picking of NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.

express 1.5.3
Dependencies: boost@1.83.0 bamtools@2.5.2 protobuf@3.21.9 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://bio.math.berkeley.edu/eXpress
Licenses: Artistic License 2.0
Build system: cmake
Synopsis: Streaming quantification for high-throughput genomic sequencing
Description:

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.

mosaicatcher 0.3.1
Dependencies: boost@1.89.0 htslib@1.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/friendsofstrandseq/mosaicatcher
Licenses: Expat
Build system: cmake
Synopsis: Count and classify Strand-seq reads
Description:

Mosaicatcher counts Strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.

ngs-bits 2025_09
Dependencies: bzip2@1.0.8 curl@8.6.0 htslib@1.21 libdeflate@1.19 libxml2@2.14.6 lzip@1.25 openssl@3.0.8 qtbase@5.15.17 qtsvg@5.15.17 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/imgag/ngs-bits
Licenses: Expat
Build system: gnu
Synopsis: Short-read and long-read sequencing tools for diagnostics
Description:

Ngs-bits (Next-Generation Sequencing) is collection of short-read and long-read sequencing tools for diagnostics.

python-biopython 1.73
Propagated dependencies: python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biopython.org/
Licenses: non-copyleft
Build system: pyproject
Synopsis: Tools for biological computation in Python
Description:

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

python-peaks2utr 1.4.1
Propagated dependencies: python-asgiref@3.8.1 python-gffutils@0.13 python-importlib-resources@6.5.2 macs@2.2.9.1 python-numpy@1.26.4 python-psutil@7.0.0 python-pybedtools@0.10.0 python-pysam@0.23.0 python-requests@2.32.5 python-tqdm@4.67.1 python-typing-extensions@4.15.0 python-zipp@3.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haessar/peaks2utr
Licenses: GPL 3+
Build system: pyproject
Synopsis: Python CLI for annotating three prime UTR
Description:

This package provides a robust, parallelized Python CLI for annotating three prime UTR.

python-bioframe 0.6.4
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-pyyaml@6.0.2 python-requests@2.32.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/open2c/bioframe
Licenses: Expat
Build system: pyproject
Synopsis: Pandas utilities for tab-delimited and other genomic files
Description:

This package is a library to enable flexible and scalable operations on genomic interval dataframes in Python. Bioframe enables access to a rich set of dataframe operations. Working in Python enables rapid visualization and iteration of genomic analyses. The philosophy underlying bioframe is to enable flexible operations. Instead of creating a function for every possible use-case, we encourage users to compose functions to achieve their goals.

r-imagearray 1.0-1.78b4b18
Propagated dependencies: r-delayedarray@0.36.0 r-hdf5array@1.38.0 r-magick@2.9.0 r-s4arrays@1.10.0 r-zarrarray@1.0-1.508d871
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/ImageArray
Licenses: Expat
Build system: r
Synopsis: DelayedArray based image operations
Description:

DelayedArray based image operations.

transanno 0.4.5
Dependencies: xz@5.4.5 zstd@1.5.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/informationsea/transanno
Licenses: GPL 3+
Build system: cargo
Synopsis: LiftOver tool for new genome assemblies
Description:

This package provides an accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies.

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