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

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-pybedtools 0.10.0
Dependencies: zlib@1.3.1
Propagated dependencies: bedtools@2.31.1 samtools@1.19 kentutils@302.0.0 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-pysam@0.23.0 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pythonhosted.org/pybedtools/
Licenses: Expat LGPL 2.1+
Build system: pyproject
Synopsis: Python wrapper for BEDtools programs
Description:

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.

r-wasabi 1.0.1-1.8c33cab
Propagated dependencies: r-data-table@1.17.8 r-rhdf5@2.54.0 r-rjson@0.2.23
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/COMBINE-lab/wasabi
Licenses: Modified BSD
Build system: r
Synopsis: Use Sailfish and Salmon with Sleuth
Description:

This package converts the output of the Sailfish and Salmon RNA-seq quantification tools so that it can be used with the Sleuth differential analysis package.

sickle 1.33
Propagated dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/najoshi/sickle
Licenses: Expat
Build system: gnu
Synopsis: Adaptive trimming tool for FASTQ files using quality
Description:

Sickle is a tool that trims reads based on quality and length thresholds. It uses sliding windows to detect low-quality bases at the 3'-end and high-quality bases at the 5'-end. Additionally, it discards reads based on the length threshold.

python-demuxem 0.1.7
Propagated dependencies: python-docopt@0.6.2 python-importlib-metadata@8.7.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pegasusio@0.9.1 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lilab-bcb/demuxEM
Licenses: Modified BSD
Build system: pyproject
Synopsis: Analyze cell-hashing/nucleus-hashing data
Description:

This is a Python module for analyzing cell-hashing/nucleus-hashing data. It is the demultiplexing module of Pegasus, which is used by Cumulus in the demultiplexing step.

pairadise 1.0.0
Dependencies: star@2.7.8a
Propagated dependencies: python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Xinglab/PAIRADISE
Licenses: GPL 3+
Build system: pyproject
Synopsis: Paired replicate analysis of allelic differential splicing events
Description:

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

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.

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.

r-readwriter 1.5.3-1.91373c4
Propagated dependencies: r-gtools@3.9.5 r-openxlsx@4.2.8.1 r-readr@2.1.6 r-stringendo@0.6.0-1.15594b1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/ReadWriter
Licenses: GPL 3
Build system: r
Synopsis: Functions to read and write files conveniently
Description:

ReadWriter is a set of R functions to read and write files conveniently.

python-mgatk 0.7.0
Propagated dependencies: python-biopython@1.85 python-click@8.1.8 python-numpy@1.26.4 python-optparse-pretty@0.1.1 python-pandas@2.2.3 python-pysam@0.23.0 python-regex@2024.11.6 python-ruamel.yaml@0.18.14 python-setuptools@80.9.0 snakemake@8.29.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/caleblareau/mgatk
Licenses: Expat
Build system: pyproject
Synopsis: Mitochondrial genome analysis toolkit
Description:

This package is a Python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. The mgatk package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

seqmagick 0.8.6-0.dee6ab9
Dependencies: python-biopython@1.85 python-pygtrie@2.5.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/fhcrc/seqmagick
Licenses: GPL 3
Build system: pyproject
Synopsis: Tools for converting and modifying sequence files
Description:

Bioinformaticians often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. Seqmagick is a utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

randfold 2.0.1
Dependencies: eddylab-squid@1.9g
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/
Licenses: GPL 2
Build system: gnu
Synopsis: Minimum free energy of folding randomization test software
Description:

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

go-github-com-biogo-store 0.0.0-20201120204734-aad293a2328f
Propagated dependencies: go-gopkg-in-check-v1@1.0.0-20201130134442-10cb98267c6c go-github-com-kr-pretty@0.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biogo/store
Licenses: Modified BSD
Build system: go
Synopsis: Interval store type for biogo
Description:

The store package provides a number of data store types that are useful for bioinformatic analysis.

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.

bpp-phyl-omics 2.4.1
Dependencies: bpp-core@2.4.1 bpp-phyl@2.4.1 bpp-seq@2.4.1 bpp-seq-omics@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BioPP/bpp-phyl-omics
Licenses: CeCILL
Build system: cmake
Synopsis: Bio++ phylogenetic library genomics components
Description:

This library contains the genomics components of the Bio++ phylogenetics library. It is part of the Bio++ project.

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.

skewer 0-1.978e8e4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/relipmoc/skewer
Licenses: Expat
Build system: gnu
Synopsis: Bit-masked k-difference matching
Description:

Skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

r-bamutils 0.0.0.9000-2.0a7d2d9
Propagated dependencies: r-abind@1.4-8 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-gutils@0.2.0-2.fc24db6 r-rsamtools@2.26.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/bamutils/
Licenses: GPL 2
Build system: r
Synopsis: Utility functions for manipulating BAMs
Description:

This package provides utility functions for manipulating BAM files.

exonerate 2.4.0
Dependencies: glib@2.83.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
Licenses: GPL 3
Build system: gnu
Synopsis: Generic tool for biological sequence alignment
Description:

Exonerate is a generic tool for pairwise sequence comparison. It allows the alignment of sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

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.

rscape 2.0.0.q
Propagated dependencies: gsl@2.8 openmpi@4.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/EddyRivasLab/R-scape
Licenses: Modified BSD
Build system: gnu
Synopsis: RNA structural covariation above phylogenetic expectation
Description:

R-scape discovers RNA secondary structure consensus elements. These elements include riboswitches and ribozymes. It utilizes probabilistic modeling of sequence alignments, explicitly considering folding dependencies. The tool enables the de novo search for new structural elements and facilitates comparative analysis of known RNA families.

r-databaselinke-r 1.7.0-1.cf3d6cc
Propagated dependencies: r-readwriter@1.5.3-1.91373c4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/DatabaseLinke.R
Licenses: GPL 3
Build system: r
Synopsis: Parse links to databases from your list of gene symbols
Description:

This package provides a set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

fastp 0.23.2
Dependencies: isa-l@2.31.1 libdeflate@1.19
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/OpenGene/fastp/
Licenses: Expat
Build system: gnu
Synopsis: All-in-one FastQ preprocessor
Description:

Fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool has multi-threading support to afford high performance.

pyscenic 0.12.1-1.eaf23eb
Propagated dependencies: python-aiohttp@3.11.11 python-arboreto@0.1.6 python-attrs@25.3.0 python-boltons@25.0.0 python-cloudpickle@3.1.0 python-ctxcore@0.2.0 python-cytoolz@1.0.1 python-dask@2024.12.1 python-distributed@2024.12.1 python-frozendict@2.4.6 python-fsspec@2025.9.0 python-interlap@0.2.7 python-llvmlite@0.44.0 python-loompy@3.0.7 python-multiprocessing-on-dill@3.5.0a4 python-networkx@3.4.2 python-numba@0.61.0 python-numexpr@2.12.1 python-numpy@1.26.4 python-pandas@2.2.3 python-pyarrow@22.0.0 python-pyyaml@6.0.2 python-requests@2.32.5 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-setuptools@80.9.0 python-tqdm@4.67.1 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://scenic.aertslab.org/
Licenses: GPL 3+
Build system: pyproject
Synopsis: Single-Cell regulatory network inference and clustering
Description:

pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

python-taggd 0.4.0
Propagated dependencies: python-numpy@1.26.4 python-pysam@0.23.0 python-tqdm@4.67.1 python-aiofiles@24.1.0 python-dnaio@0.10.0 python-types-aiofiles@25.1.0.20251011 python-types-tqdm@4.67.0.20250809
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jfnavarro/taggd
Licenses: Modified BSD
Build system: pyproject
Synopsis: Genetic barcode demultiplexing
Description:

This package provides TagGD barcode demultiplexing utilities for Spatial Transcriptomics data.

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Total results: 68655