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

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.


diamond 2.1.6
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/bbuchfink/diamond
Licenses: GPL 3+
Build system: cmake
Synopsis: Accelerated BLAST compatible local sequence aligner
Description:

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

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.

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.

indelfixer 1.1
Dependencies: java-commons-lang@2.6 java-args4j@2.33
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cbg-ethz/InDelFixer/
Licenses: GPL 3+
Build system: ant
Synopsis: Iterative and sensitive NGS sequence aligner
Description:

InDelFixer is a sensitive aligner for 454, Illumina and PacBio data, employing a full Smith-Waterman alignment against a reference. This Java command line application aligns Next-Generation Sequencing (NGS) and third-generation reads to a set of reference sequences, by a prior fast k-mer matching and removes indels, causing frame shifts. In addition, only a specific region can be considered. An iterative refinement of the alignment can be performed, by alignment against the consensus sequence with wobbles. The output is in SAM format.

htseq 2.0.2
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/htseq
Licenses: GPL 3+
Build system: pyproject
Synopsis: Framework for analyzing high-throughput sequencing data
Description:

This package provides a framework to process and analyze data from high-throughput sequencing (HTS) assays

crossmap 0.6.1
Dependencies: python-bx-python@0.14.0 python-numpy@1.26.4 python-pybigwig@0.3.22 python-pysam@0.23.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://crossmap.sourceforge.net/
Licenses: GPL 2+
Build system: pyproject
Synopsis: Convert genome coordinates between assemblies
Description:

CrossMap is a program for conversion of genome coordinates or annotation files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

r-illuminahumanmethylationepicanno-ilm10b5-hg38 0.0.1-1.3db0691
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Human Methylation EPIC Annotation version 1.0B5
Description:

This package provides a companion annotation file to the IlluminaHumanMethylationEPICmanifest package based on the same annotation 1.0B5.

r-genenmf 0.9.2-1.7ac4752
Propagated dependencies: r-cluster@2.1.8.1 r-colorspace@2.1-2 r-dendextend@1.19.1 r-irlba@2.3.5.1 r-lsa@0.73.3 r-matrix@1.7-4 r-pheatmap@1.0.13 r-rcppml@0.3.7 r-seurat@5.3.1 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/carmonalab/GeneNMF
Licenses: GPL 3
Build system: r
Synopsis: Non-Negative matrix factorization for single-cell omics
Description:

This package provides a collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). GeneNMF contains functions to directly interact with the Seurat toolkit and derive interpretable gene program signatures.

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.

discrover 1.6.0
Dependencies: boost@1.89.0 cairo@1.18.4 rmath-standalone@4.5.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://dorina.mdc-berlin.de/public/rajewsky/discrover/
Licenses: GPL 3+
Build system: cmake
Synopsis: Discover discriminative nucleotide sequence motifs
Description:

Discrover is a motif discovery method to find binding sites of nucleic acid binding proteins.

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-pybigwig 0.3.22
Dependencies: libbigwig@0.4.4 zlib@1.3.1 curl@8.6.0
Propagated dependencies: python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dpryan79/pyBigWig
Licenses: Expat
Build system: pyproject
Synopsis: Access bigWig files in Python using libBigWig
Description:

This package provides Python bindings to the libBigWig library for accessing bigWig files.

python-bwapy 0.1.4
Dependencies: zlib@1.3.1
Propagated dependencies: python-cffi@1.17.1 python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ACEnglish/bwapy
Licenses: MPL 2.0
Build system: pyproject
Synopsis: Python bindings to bwa aligner
Description:

This package provides Python bindings to the bwa mem aligner.

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.

r-pando 1.0.5
Propagated dependencies: r-bayestestr@0.17.0 r-foreach@1.5.2 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggpointdensity@0.2.1 r-ggraph@2.2.2 r-glmnetutils@1.1.9 r-grr@0.9.5 r-iranges@2.44.0 r-irlba@2.3.5.1 r-matrix@1.7-4 r-matrixgenerics@1.22.0 r-motifmatchr@1.32.0 r-pals@1.10 r-patchwork@1.3.2 r-seurat@5.3.1 r-signac@1.12.0-1.8ecdde2 r-sparsematrixstats@1.22.0 r-tfbstools@1.48.0 r-tidygraph@1.3.1 r-tidyverse@2.0.0 r-uwot@0.2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/quadbiolab/Pando
Licenses: Expat
Build system: r
Synopsis: Infer regulomes from multi-modal single-cell genomics data
Description:

Pando leverages multi-modal single-cell measurements to infer gene regulatory networks using a flexible linear model-based framework. By modeling the relationship between TF-binding site pairs with the expression of target genes, Pando simultaneously infers gene modules and sets of regulatory regions for each transcription factor.

mash 2.3
Dependencies: capnproto@1.2.0 htslib@1.21 gsl@2.8 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://mash.readthedocs.io
Licenses: Modified BSD Expat Public Domain CPL 1.0
Build system: gnu
Synopsis: Fast genome and metagenome distance estimation using MinHash
Description:

Mash is a fast sequence distance estimator that uses the MinHash algorithm and is designed to work with genomes and metagenomes in the form of assemblies or reads.

python-pyspoa 0.0.5
Propagated dependencies: pybind11@2.13.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nanoporetech/pyspoa
Licenses: Expat
Build system: python
Synopsis: Python bindings for the SIMD partial order alignment library
Description:

This package provides Python bindings for spoa, a C++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences

seqan 3.0.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Build system: cmake
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.

bbmap 39.01
Dependencies: gawk@5.3.0 java-eclipse-jdt-core@3.16.0 java-eclipse-jdt-compiler-apt@1.3.400 java-openmpi@4.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/bbmap/
Licenses: Modified BSD
Build system: ant
Synopsis: Aligner and other tools for short sequencing reads
Description:

This package provides bioinformatic tools to align, deduplicate, reformat, filter and normalize DNA and RNA-seq data. It includes the following tools: BBMap, a short read aligner for DNA and RNA-seq data; BBNorm, a kmer-based error-correction and normalization tool; Dedupe, a tool to simplify assemblies by removing duplicate or contained subsequences that share a target percent identity; Reformat, to convert reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s; and BBDuk, a tool to filter, trim, or mask reads with kmer matches to an artifact/contaminant file.

python-biofluff 3.0.4
Propagated dependencies: htseq@2.0.2 python-matplotlib@3.8.2 python-numpy@1.26.4 python-palettable@3.3.3 python-pybedtools@0.10.0 python-pybigwig@0.3.22 python-pysam@0.23.0 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/simonvh/fluff/
Licenses: Expat
Build system: pyproject
Synopsis: Analysis and visualization of high-throughput sequencing data
Description:

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

r-kbet 0.99.6-1.f35171d
Propagated dependencies: r-cluster@2.1.8.1 r-fnn@1.1.4.1 r-ggplot2@4.0.1 r-mass@7.3-65 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/theislab/kBET
Licenses: GPL 3+
Build system: r
Synopsis: k-nearest neighbour batch effect test
Description:

This tool detects batch effects in high-dimensional data based on chi^2-test.

python-decoupler 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.

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