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

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-episcanpy 0.4.0
Propagated dependencies: python-anndata@0.11.4 python-bamnostic@1.1.8 python-h5py@3.13.0 python-intervaltree@3.1.0 python-joblib@1.5.2 python-kneed@0.8.5 python-legacy-api-wrap@1.4.1 python-matplotlib@3.8.2 python-natsort@8.4.0 python-networkx@3.4.2 python-numba@0.61.0 python-numpy@1.26.4 python-packaging@25.0 python-pandas@2.2.3 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-statsmodels@0.14.4 python-tqdm@4.67.1 python-pysam@0.23.0 python-tbb@2021.6.0 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/colomemaria/epiScanpy
Licenses: Modified BSD
Build system: pyproject
Synopsis: Tool for epigenomics single cell analysis
Description:

EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018).

sra-tools 2.10.6
Dependencies: ngs-sdk@2.10.5 ncbi-vdb@2.10.6 file@5.46 fuse@2.9.9 hdf5@1.10.9 libxml2@2.14.6 zlib@1.3.1 python-wrapper@3.11.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
Licenses: Public Domain
Build system: gnu
Synopsis: Tools and libraries for reading and writing sequencing data
Description:

The SRA Toolkit from NCBI is a collection of tools and libraries for reading of sequencing files from the Sequence Read Archive (SRA) database and writing files into the .sra format.

fsom 0.0.0-1.a6ef318
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/fsom
Licenses: GPL 3
Build system: gnu
Synopsis: Manage SOM (Self-Organizing Maps) neural networks
Description:

A tiny C library for managing SOM (Self-Organizing Maps) neural networks.

sambamba 0.8.2
Dependencies: ldc@1.38.0 lz4@1.10.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biod/sambamba
Licenses: GPL 2+
Build system: gnu
Synopsis: Tools for working with SAM/BAM data
Description:

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.

java-forester 0-1.86b07ef
Propagated dependencies: java-commons-codec@1.15 java-openchart2@1.4.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sites.google.com/site/cmzmasek/home/software/forester
Licenses: LGPL 2.1+
Build system: ant
Synopsis: Phylogenomics libraries for Java
Description:

Forester is a collection of Java libraries for phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.

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.

python-weblogo 3.7.12
Propagated dependencies: ghostscript@9.56.1 python-numpy@1.26.4 python-pluggy@1.6.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/gecrooks/weblogo
Licenses: Expat
Build system: pyproject
Synopsis: Sequence Logo Generator
Description:

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

WebLogo can create output in several common graphics' formats, including the bitmap formats GIF and PNG, suitable for on-screen display, and the vector formats EPS and PDF, more suitable for printing, publication, and further editing. Additional graphics options include bitmap resolution, titles, optional axis, and axis labels, antialiasing, error bars, and alternative symbol formats.

A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position.

newick-utils 1.6-1.da121155
Dependencies: libxml2@2.14.6 flex@2.6.4 bison@3.8.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tjunier/newick_utils
Licenses: Modified BSD
Build system: gnu
Synopsis: Programs for working with newick format phylogenetic trees
Description:

Newick-utils is a suite of utilities for processing phylogenetic trees in Newick format. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).

java-forester 1.005
Propagated dependencies: java-commons-codec@1.15 java-openchart2@1.4.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sites.google.com/site/cmzmasek/home/software/forester
Licenses: LGPL 2.1+
Build system: ant
Synopsis: Phylogenomics libraries for Java
Description:

Forester is a collection of Java libraries for phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.

r-seuratextenddata 0.2.1-1.e7f17d4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huayc09/SeuratExtendData
Licenses: GPL 3+
Build system: r
Synopsis: Data attached to SeuratExtend package
Description:

This package provides data for the SeuratExtend tool.

r-xbioc 0.1.16-1.6ff0670
Propagated dependencies: r-annotationdbi@1.72.0 r-assertthat@0.2.1 r-biobase@2.70.0 r-biocmanager@1.30.27 r-digest@0.6.39 r-pkgmaker@0.32.10 r-plyr@1.8.9 r-reshape2@1.4.5 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/renozao/xbioc/
Licenses: GPL 3+
Build system: r
Synopsis: Extra base functions for Bioconductor
Description:

This package provides extra utility functions to perform common tasks in the analysis of omics data, leveraging and enhancing features provided by Bioconductor packages.

python-bamnostic 1.1.8
Propagated dependencies: python-pytest@8.4.1 python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/betteridiot/bamnostic/
Licenses: Modified BSD
Build system: pyproject
Synopsis: Tool for binary alignment map, random access and parsing
Description:

Bamnostic is a pure Python Binary Alignment Map (BAM) file parser and random access tool.

raxml 8.2.12
Dependencies: openmpi@4.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://cme.h-its.org/exelixis/web/software/raxml/index.html
Licenses: GPL 2+
Build system: gnu
Synopsis: Randomized Axelerated Maximum Likelihood phylogenetic trees
Description:

RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.

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.

r-seraster 0.99.0-1.4fdc1ff
Propagated dependencies: r-biocparallel@1.44.0 r-ggplot2@4.0.1 r-matrix@1.7-4 r-rearrr@0.3.5 r-sf@1.0-23 r-spatialexperiment@1.20.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/JEFworks-Lab/SEraster
Licenses: GPL 3
Build system: r
Synopsis: Rasterization framework for scalable spatial omics data analysis
Description:

This package is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of points in spatial omics datasets for downstream analysis through a process of rasterization where single cells gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.

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.

python-schema-salad 8.9.20250723145140
Propagated dependencies: python-cachecontrol@0.14.1 python-mistune@3.1.3 python-mypy-extensions@1.1.0 python-rdflib@7.1.1 python-requests@2.32.5 python-ruamel.yaml@0.18.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/common-workflow-language/schema_salad
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Schema Annotations for Linked Avro Data (SALAD)
Description:

Salad is a schema language for describing JSON or YAML structured linked data documents. Salad schema describes rules for preprocessing, structural validation, and hyperlink checking for documents described by a Salad schema. Salad supports rich data modeling with inheritance, template specialization, object identifiers, object references, documentation generation, code generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.

circtools 1.0.0
Dependencies: bioparser@3.0.13 biosoup@0.10.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Kevinzjy/circtools
Licenses: Expat
Build system: cargo
Synopsis: Accelerating functions in CIRI toolkit
Description:

This package provides accelerated functions for the CIRI toolkit. It also provides the ccs executable to scan for circular consensus sequences.

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.

python-decoupler-py 2.1.1
Propagated dependencies: python-adjusttext@1.3.0 python-anndata@0.12.1 python-dcor@0.6 python-docrep@0.3.2 python-igraph@0.11.8 python-ipywidgets@8.1.2 python-marsilea@0.5.4 python-numba@0.61.0 python-requests@2.32.5 python-scipy@1.12.0 python-session-info2@0.2 python-tqdm@4.67.1 python-xgboost@1.7.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/scverse/decoupler
Licenses: Modified BSD
Build system: pyproject
Synopsis: Framework for modeling, analyzing and interpreting single-cell RNA-seq data
Description:

This package provides different statistical methods to extract biological activities from omics data within a unified framework.

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.

phyml 3.3.20220408
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/stephaneguindon/phyml
Licenses: GPL 3
Build system: gnu
Synopsis: Programs for working on SAM/BAM files
Description:

PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled with efficient options to search the space of phylogenetic tree topologies. codePhyREX fits the spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model is similar to the structured coalescent but assumes that individuals are distributed along a spatial continuum rather than discrete demes. PhyREX can be used to estimate population densities and rates of dispersal. Its output can be processed by treeannotator (from the BEAST package) as well as SPREAD.

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.

instrain 1.10.0-0.6180be7
Propagated dependencies: python-biopython@1.73 python-h5py@3.13.0 python-lmfit@1.3.4 python-matplotlib@3.8.2 python-networkx@3.4.2 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-pysam@0.23.0 python-seaborn@0.13.2 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/MrOlm/inStrain
Licenses: Expat
Build system: pyproject
Synopsis: Calculation of strain-level metrics
Description:

inStrain is a Python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.

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Total results: 68658