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

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-ete3 3.1.3
Propagated dependencies: python-lxml@6.0.1 python-numpy@1.26.4 python-pyqt@5.15.11 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://etetoolkit.org
Licenses: GPL 3+
Build system: pyproject
Synopsis: Python environment for phylogenetic tree exploration
Description:

This package provides a Python environment for phylogenetic tree exploration.

vembrane 1.0.7
Dependencies: python-asttokens@3.0.0 python-intervaltree@3.1.0 python-numpy@1.26.4 python-pysam@0.23.0 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vembrane/vembrane
Licenses: Expat
Build system: pyproject
Synopsis: Filter VCF/BCF files with Python expressions
Description:

Vembrane simultaneously filters variants based on any INFO or FORMAT field, CHROM, POS, ID, REF, ALT, QUAL, FILTER, and the annotation field ANN. When filtering based on ANN, annotation entries are filtered first. If no annotation entry remains, the entire variant is deleted.

r-p2data 1.0.0-1.7d4c0e1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/kharchenkolab/p2data
Licenses: GPL 3
Build system: r
Synopsis: Data for pagoda2
Description:

This package contains data used by pagoda2. The data within this package are the 3000 bone marrow cells used for vignettes.

java-biojava-core 4.2.11
Propagated dependencies: java-log4j-api@2.17.1 java-log4j-core@2.17.1 java-slf4j-api@1.7.25 java-slf4j-simple@1.7.25
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biojava.org
Licenses: LGPL 2.1+
Build system: ant
Synopsis: Core libraries of Java framework for processing biological data
Description:

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

r-dropbead 0-2.d746c6f
Propagated dependencies: r-ggplot2@4.0.1 r-rcolorbrewer@1.1-3 r-gridextra@2.3 r-gplots@3.2.0 r-plyr@1.8.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rajewsky-lab/dropbead
Licenses: GPL 3
Build system: r
Synopsis: Basic exploration and analysis of Drop-seq data
Description:

This package offers a quick and straight-forward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.

wfa2-lib 2.3.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/smarco/WFA2-lib
Licenses: Expat
Build system: cmake
Synopsis: Wavefront alignment algorithm library
Description:

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.

seek 1-1.196ed4c
Dependencies: apache-thrift@0.14.2 apache-thrift@0.14.2 gsl@2.8 boost@1.89.0 gengetopt@2.23 libsvm@336 log4cpp@1.1.3 python@3.11.14 readline@8.2.13
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://seek.princeton.edu
Licenses: CC-BY 3.0
Build system: cmake
Synopsis: Gene co-expression search engine
Description:

SEEK is a computational gene co-expression search engine. SEEK provides biologists with a way to navigate the massive human expression compendium that now contains thousands of expression datasets. SEEK returns a robust ranking of co-expressed genes in the biological area of interest defined by the user's query genes. It also prioritizes thousands of expression datasets according to the user's query of interest.

stpipeline 2.0.0
Propagated dependencies: htseq@2.0.2 python-distance@0.1.3-0.ad7f9dc python-dnaio@0.10.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0 python-regex@2024.11.6 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-taggd@0.4.0 python-types-regex@2025.9.18.20250921 samtools@1.19 star@2.7.8a
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jfnavarro/st_pipeline
Licenses: Expat
Build system: pyproject
Synopsis: Pipeline for spatial mapping of unique transcripts
Description:

This package provides an automated pipeline for spatial mapping of unique transcripts.

proteinortho 6.3.2
Dependencies: bash-minimal@5.2.37 guile@3.0.9 diamond@2.1.6 perl@5.36.0 python-wrapper@3.11.14 blast+@2.17.0 openblas@0.3.30
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinf.uni-leipzig.de/Software/proteinortho
Licenses: GPL 3+
Build system: gnu
Synopsis: Detect orthologous genes across species
Description:

Proteinortho is a tool to detect orthologous genes across different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.

r-doubletfinder 2.0.3-1.554097b
Propagated dependencies: r-fields@17.1 r-kernsmooth@2.23-26 r-rocr@1.0-11
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/chris-mcginnis-ucsf/DoubletFinder
Licenses: CC0
Build system: r
Synopsis: Identify doublets in single-cell RNA sequencing data
Description:

DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires optimal pK selection and homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.

r-maxprobes 0.0.2-1.c2120db
Propagated dependencies: r-minfi@1.56.0 r-minfidata@0.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/markgene/maxprobes
Licenses: GPL 2+
Build system: r
Synopsis: Methylation array cross-reactive probes
Description:

The Maxprobes package collects cross-reactive probes of Illumina methylation array 450K and EPIC/850K.

python-cellbender 0.2.2
Propagated dependencies: python-anndata@0.12.1 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-pyro-ppl@1.9.1 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-sphinx@7.4.7 python-sphinx-argparse@0.5.2 python-sphinx-autodoc-typehints@1.25.3 python-sphinx-rtd-theme@3.0.2 python-sphinxcontrib-programoutput@0.17 python-tables@3.10.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://cellbender.rtfd.io/
Licenses: Modified BSD
Build system: pyproject
Synopsis: Eliminate technical artifacts from single-cell RNA-seq data
Description:

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

gdc-client 2.3
Dependencies: python-importlib-metadata@8.7.0 python-intervaltree@3.1.0 python-jsonschema@4.23.0 python-lxml@6.0.1 python-progressbar2@4.5.0 python-pyyaml@6.0.2 python-requests@2.32.5 python-termcolor@2.5.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool
Licenses: ASL 2.0
Build system: pyproject
Synopsis: GDC data transfer tool
Description:

The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

imp 2.23.0
Dependencies: boost@1.59.0 cereal@1.3.2 cgal@5.6.1 gsl@2.8 hdf5@1.14.6 fftw@3.3.10 eigen@3.4.0 opencv@4.12.0
Propagated dependencies: python-numpy@1.26.4 python-scipy@1.12.0 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-networkx@3.4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://integrativemodeling.org
Licenses: LGPL 2.1+ GPL 3+
Build system: cmake
Synopsis: Integrative modeling platform
Description:

IMP's broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. IMP provides a C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way.

bioruby 2.0.4
Propagated dependencies: ruby-libxml@5.0.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://bioruby.org/
Licenses: Ruby License LGPL 2.1+ GPL 2+
Build system: ruby
Synopsis: Ruby library, shell and utilities for bioinformatics
Description:

BioRuby comes with a comprehensive set of Ruby development tools and libraries for bioinformatics and molecular biology. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.

python-fastalite 0.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nhoffman/fastalite
Licenses: Expat
Build system: pyproject
Synopsis: Simplest possible FASTA parser
Description:

This library implements a FASTA and a FASTQ parser without relying on a complex dependency tree.

htslib 1.21
Dependencies: bzip2@1.0.8 curl@8.6.0 openssl@3.0.8 xz@5.4.5
Propagated dependencies: htscodecs@1.6.1 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.htslib.org
Licenses: Expat Modified BSD
Build system: gnu
Synopsis: C library for reading/writing high-throughput sequencing data
Description:

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

java-biojava-phylo 4.0.0
Propagated dependencies: java-log4j-api@2.17.1 java-log4j-core@2.17.1 java-slf4j-api@1.7.25 java-slf4j-simple@1.7.25 java-biojava-core@4.0.0 java-forester@1.005
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biojava.org
Licenses: LGPL 2.1+
Build system: ant
Synopsis: Biojava interface to the forester phylogenomics library
Description:

The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees.

python-vireosnp 0.5.9-0.e365463
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huangyh09/vireoSNP
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Deconvolution based on SNP for multiplexed scRNA-seq data
Description:

This package provides a deconvolution based on Single Nucleotide Position (SNP) for multiplexed scRNA-seq data. The name vireo stand for Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data and follows the clone identification from single-cell data named cardelino.

flair 1.6.4
Dependencies: bash-minimal@5.2.37 r-minimal@4.5.2 r-apeglm@1.32.0 r-deseq2@1.50.2 r-drimseq@1.38.0 r-ggplot2@4.0.1 r-lazyeval@0.2.2 r-qqman@0.1.9 r-rlang@1.1.6
Propagated dependencies: python-mappy@2.24 python-numpy@1.26.4 python-ncls@0.0.68 python-pybedtools@0.10.0 python-pysam@0.23.0 python-rpy2@3.5.17 python-scipy@1.12.0 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://flair.readthedocs.io/en/latest/
Licenses: Modified BSD
Build system: python
Synopsis: Full-length alternative isoform analysis of RNA
Description:

This package implements FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.

plink-ng 2.0.0-a.6.16
Dependencies: libdeflate@1.19 openblas@0.3.30 zlib@1.3.1 zstd@1.5.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.cog-genomics.org/plink/
Licenses: GPL 3+
Build system: gnu
Synopsis: Whole genome association analysis toolset
Description:

PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

r-demultiplex 1.0.2-1.6e2a142
Propagated dependencies: r-kernsmooth@2.23-26 r-reshape2@1.4.5 r-rtsne@0.17 r-shortread@1.68.0 r-stringdist@0.9.15
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/chris-mcginnis-ucsf/MULTI-seq
Licenses: CC0
Build system: r
Synopsis: MULTI-seq pre-processing and classification tools
Description:

deMULTIplex is an R package for analyzing single-cell RNA sequencing data generated with the MULTI-seq sample multiplexing method. The package includes software to

  1. Convert raw MULTI-seq sample barcode library FASTQs into a sample barcode UMI count matrix, and

  2. Classify cell barcodes into sample barcode groups.

r-spacexr 2.2.1-1.0a0861e
Propagated dependencies: r-compquadform@1.4.4 r-data-table@1.17.8 r-doparallel@1.0.17 r-dplyr@1.1.4 r-fields@17.1 r-foreach@1.5.2 r-ggplot2@4.0.1 r-knitr@1.50 r-locfdr@1.1-8 r-matrix@1.7-4 r-metafor@4.8-0 r-mgcv@1.9-4 r-pals@1.10 r-quadprog@1.5-8 r-readr@2.1.6 r-reshape2@1.4.5 r-rfast@2.1.5.2 r-rmarkdown@2.30 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dmcable/spacexr
Licenses: GPL 3
Build system: r
Synopsis: Cell type identification and differential expression in spatial transcriptomics
Description:

This package is used for cell type identification in spatial transcriptomics. It also handles cell type-specific differential expression.

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Total results: 68655