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

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-dnaio 0.10.0
Propagated dependencies: python-xopen@1.8.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/marcelm/dnaio/
Licenses: Expat
Build system: pyproject
Synopsis: Read FASTA and FASTQ files efficiently
Description:

dnaio is a Python library for fast parsing of FASTQ and also FASTA files. The code was previously part of the cutadapt tool.

bowtie1 1.3.1
Dependencies: python-wrapper@3.11.14 tbb@2021.6.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bowtie-bio.sourceforge.net/index.shtml
Licenses: Artistic License 2.0
Build system: gnu
Synopsis: Fast aligner for short nucleotide sequence reads
Description:

Bowtie is a fast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

python-pypairix 0.3.9
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/4dn-dcic/pairix
Licenses: Expat
Build system: pyproject
Synopsis: Support for querying pairix-indexed bgzipped text files
Description:

Pypairix is a Python module for fast querying on a pairix-indexed bgzipped text file that contains a pair of genomic coordinates per line.

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.

bppsuite 2.4.1
Dependencies: bpp-core@2.4.1 bpp-seq@2.4.1 bpp-phyl@2.4.1 bpp-popgen@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BioPP
Licenses: CeCILL-C
Build system: cmake
Synopsis: Bioinformatics tools written with the Bio++ libraries
Description:

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This package provides command line tools using the Bio++ library.

bio-blastxmlparser 2.0.4
Dependencies: ruby-rspec@3.13.1
Propagated dependencies: ruby-bio-logger@1.0.1 ruby-nokogiri@1.18.10
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pjotrp/blastxmlparser
Licenses: Expat
Build system: ruby
Synopsis: Fast big data BLAST XML parser and library
Description:

Very fast parallel big-data BLAST XML file parser which can be used as command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.

genrich 0.5
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jsh58/Genrich
Licenses: Expat
Build system: gnu
Synopsis: Detecting sites of genomic enrichment
Description:

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

fastqc 0.11.9
Dependencies: icedtea@3.19.0 java-cisd-jhdf5@14.12.6-39162 java-picard@1.113 java-jbzip2@0.9.1 perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Licenses: GPL 3+
Build system: ant
Synopsis: Quality control tool for high throughput sequence data
Description:

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are:

  • Import of data from BAM, SAM or FastQ files (any variant);

  • Providing a quick overview to tell you in which areas there may be problems;

  • Summary graphs and tables to quickly assess your data;

  • Export of results to an HTML based permanent report;

  • Offline operation to allow automated generation of reports without running the interactive application.

phylip 3.697
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://evolution.genetics.washington.edu/phylip/
Licenses: FreeBSD
Build system: gnu
Synopsis: Tools for inferring phylogenies
Description:

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).

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.

r-gtrack 0.1.0-1.a694fa3
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gutils@0.2.0-2.fc24db6 r-iranges@2.44.0 r-matrix@1.7-4 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-rcurl@1.98-1.17 r-rtracklayer@1.70.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/gTrack/
Licenses: GPL 2
Build system: r
Synopsis: Plot tracks of complex genomic data across multiple genomic windows
Description:

This package provides an object for plotting GRanges, RleList, UCSC file formats, and ffTrack objects in multi-track panels.

python-py2bit 0.3.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dpryan79/py2bit
Licenses: Expat
Build system: pyproject
Synopsis: Access 2bit files using lib2bit
Description:

This package provides Python bindings for lib2bit to access 2bit files with Python.

python-pyvcf3 1.0.3-0.1fb3789
Propagated dependencies: python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dridk/PyVCF3
Licenses: Expat
Build system: pyproject
Synopsis: Variant Call Format parser for Python
Description:

This package provides a VCF parser for Python.

mageck 0.5.9.5
Dependencies: python-numpy@1.26.4 python-scipy@1.12.0 python-matplotlib@3.8.2 python-statsmodels@0.14.4 python-pyqt@5.15.11 r-minimal@4.5.2 r-xtable@1.8-4 r-gplots@3.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/mageck/
Licenses: Modified BSD
Build system: pyproject
Synopsis: Model-based analysis of genome-wide CRISPR-Cas9 Knockout
Description:

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. Its features include:

  1. Simple, easy to use pipeline to screen genes in Genome-wide CRISPR-Cas9 Knockout experiments;

  2. High sensitivity and low false discovery rate;

  3. Fully utilize the screening data by performing both positive and negative screening in one dataset;

  4. Provide statistical evaluation in genes, sgRNAs and pathways;

  5. Require as few as 2 samples;

  6. Identify cell-type specific targets;

  7. A set of visualization features that generate publication standard figures.

hisat2 2.2.1
Dependencies: python-wrapper@3.11.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://daehwankimlab.github.io/hisat2/
Licenses: GPL 3+
Build system: gnu
Synopsis: Graph-based alignment of genomic sequencing reads
Description:

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). In addition to using one global graph FM (GFM) index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes, combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

infernal 1.1.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://eddylab.org/infernal/
Licenses: Modified BSD
Build system: gnu
Synopsis: Inference of RNA alignments
Description:

Infernal ("INFERence of RNA ALignment") is a tool for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

checkm 1.1.3
Dependencies: python-dendropy@4.5.1 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pysam@0.23.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ecogenomics.github.io/CheckM/
Licenses: GPL 3+
Build system: pyproject
Synopsis: Assess the quality of putative genome bins
Description:

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.

smithlab-cpp 0.1.728a097
Dependencies: samtools@0.1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/smithlabcode/smithlab_cpp
Licenses: GPL 3+
Build system: gnu
Synopsis: C++ helper library for functions used in Smith lab projects
Description:

Smithlab CPP is a C++ library that includes functions used in many of the Smith lab bioinformatics projects, such as a wrapper around Samtools data structures, classes for genomic regions, mapped sequencing reads, etc.

python-liana-py 1.6.0
Propagated dependencies: python-anndata@0.12.1 python-cell2cell@0.7.4 python-decoupler@2.1.1 python-hypothesis@6.135.26 python-ipykernel@6.29.4 python-ipython@8.37.0 python-mudata@0.3.2 python-nbconvert@7.16.6 python-nbsphinx@0.8.8 python-numpy@1.26.4 python-numpydoc@1.5.0 python-omnipath@1.0.10 python-pandas@2.2.3 python-plotnine@0.14.5 python-pypandoc@1.15 python-scipy@1.12.0 python-requests@2.32.5 python-scanpy@1.11.2 python-statsmodels@0.14.4 python-tqdm@4.67.1 tzdata@2025a
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saezlab/liana-py
Licenses: GPL 3+
Build system: pyproject
Synopsis: LIANA is a ligand-receptor analysis framework
Description:

This is a Ligand-Receptor inference framework. The framework enables the use of any LR method with any resources.

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.

macs 2.2.9.1
Propagated dependencies: python-cython@0.29.37 python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/macs3-project/MACS
Licenses: Modified BSD
Build system: pyproject
Synopsis: Model based analysis for ChIP-Seq data
Description:

MACS is an implementation of a ChIP-Seq analysis algorithm for identifying transcript factor binding sites named Model-based Analysis of ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and it improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

java-picard 2.10.3
Propagated dependencies: java-htsjdk@2.10.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://broadinstitute.github.io/picard/
Licenses: Expat
Build system: ant
Synopsis: Tools for manipulating high-throughput sequencing data and formats
Description:

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.

r-centipede 1.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://centipede.uchicago.edu/
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Predict transcription factor binding sites
Description:

CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a set of candidate binding sites, and then aims to classify the sites according to whether each site is bound or not bound by a transcription factor. CENTIPEDE is an unsupervised learning algorithm that discriminates between two different types of motif instances using as much relevant information as possible.

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Total results: 69112