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

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-pyfaidx 0.7.2.1
Propagated dependencies: python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://mattshirley.com
Licenses: Modified BSD
Build system: pyproject
Synopsis: Random access to fasta subsequences
Description:

This package provides procedures for efficient pythonic random access to fasta subsequences.

filtlong 0.2.0-1.d1bb46d
Dependencies: bash-minimal@5.2.37 gawk@5.3.0 python-wrapper@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rrwick/Filtlong/
Licenses: GPL 3 ASL 2.0
Build system: gnu
Synopsis: Tool for quality filtering of Nanopore and PacBio data
Description:

The Filtlong package is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

fxtract 2.3
Dependencies: pcre@8.45 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ctSkennerton/fxtract
Licenses: Expat
Build system: gnu
Synopsis: Extract sequences from FASTA and FASTQ files
Description:

Fxtract extracts sequences from a protein or nucleotide fastx (FASTA or FASTQ) file given a subsequence. It uses a simple substring search for basic tasks but can change to using POSIX regular expressions, PCRE, hash lookups or multi-pattern searching as required. By default fxtract looks in the sequence of each record but can also be told to look in the header, comment or quality sections.

python-ctxcore 0.2.0
Propagated dependencies: python-cytoolz@1.0.1 python-frozendict@2.4.6 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pyarrow@22.0.0 python-pyyaml@6.0.2 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aertslab/ctxcore
Licenses: GPL 3+
Build system: pyproject
Synopsis: Core functions for pycisTarget and the SCENIC tool suite
Description:

ctxcore is part of the SCENIC suite of tools. It provides core functions for pycisTarget and SCENIC.

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.

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-seqgl 1.1.4
Propagated dependencies: r-biostrings@2.78.0 r-chipkernels@1.1-1.c9cfcac r-genomicranges@1.62.0 r-spams@2.6.1 r-wgcna@1.73 r-fastcluster@1.3.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ManuSetty/SeqGL
Licenses: GPL 2+
Build system: r
Synopsis: Group lasso for Dnase/ChIP-seq data
Description:

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.

seqtk 1.3
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lh3/seqtk
Licenses: Expat
Build system: gnu
Synopsis: Toolkit for processing biological sequences in FASTA/Q format
Description:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be optionally compressed by gzip.

python-pyahocorasick 2.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/WojciechMula/pyahocorasick
Licenses: Modified BSD
Build system: pyproject
Synopsis: Library for finding multiple key strings in text
Description:

Pyahocorasick is a fast, memory-efficient library for multi-pattern string search. This means that you can find multiple key strings occurrences at once in some input text.

rsem 1.3.3
Dependencies: bash-minimal@5.2.37 boost@1.83.0 r-minimal@4.5.2 perl@5.36.0 htslib@1.3.1 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://deweylab.biostat.wisc.edu/rsem/
Licenses: GPL 3+
Build system: gnu
Synopsis: Estimate gene expression levels from RNA-Seq data
Description:

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides a user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, it can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

r-liana 0.1.14-1.6cab46c
Propagated dependencies: r-basilisk@1.22.0 r-basilisk-utils@1.22.0 r-complexheatmap@2.26.0 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-magrittr@2.0.4 r-omnipathr@3.15.3 r-purrr@1.2.0 r-rcolorbrewer@1.1-3 r-readr@2.1.6 r-reticulate@1.44.1 r-rlang@1.1.6 r-scater@1.38.0 r-scran@1.38.0 r-scuttle@1.20.0 r-seuratobject@5.2.0 r-singlecellexperiment@1.32.0 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-tidyselect@1.2.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saezlab/liana/
Licenses: GPL 3
Build system: r
Synopsis: LIANA: a LIgand-receptor ANalysis frAmework
Description:

LIANA provides a number of methods and resource for ligand-receptor interaction inference from scRNA-seq data.

biosoup 0.10.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rvaser/biosoup
Licenses: Expat
Build system: cmake
Synopsis: C++ support library for bioinformatics tools
Description:

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

go-github-com-biogo-hts 1.4.4
Propagated dependencies: go-github-com-ulikunitz-xz@0.5.12 go-github-com-kortschak-utter@1.7.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biogo/hts
Licenses: Modified BSD
Build system: go
Synopsis: HTS module for biogo
Description:

This package provides tools for handling BAM, SAM, Tabix, bgzf, CRAM, CSIv1, CSIv2 and FAI files.

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.

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.

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.

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.

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.

homer 4.11.1
Dependencies: perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://homer.ucsd.edu/homer
Licenses: GPL 3+
Build system: gnu
Synopsis: Motif discovery and next generation sequencing analysis
Description:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

python-circe 0.3.8
Dependencies: lapack@3.12.1 openblas@0.3.30
Propagated dependencies: python-anndata@0.12.1 python-dask@2024.12.1 python-distributed@2024.12.1 python-joblib@1.5.2 python-numpy@1.26.4 python-pandas@2.2.3 python-rich@13.7.1 python-scanpy@1.11.2 python-scikit-learn@1.7.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cantinilab/circe
Licenses: GPL 3
Build system: pyproject
Synopsis: Cis-regulatory interactions between chromatin regions
Description:

Circe is a Python package for inferring co-accessibility networks from single-cell ATAC-seq data, using skggm for the graphical lasso and python-scanpy for data processing.

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.

python-pyliftover 0.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/konstantint/pyliftover
Licenses: Expat
Build system: pyproject
Synopsis: Python implementation of UCSC liftOver genome coordinate conversion
Description:

PyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.

r-netid 0.1.0-1.6ad1ffd
Propagated dependencies: r-doparallel@1.0.17 r-dorng@1.8.6.2 r-glmnet@4.1-10 r-hmisc@5.2-4 r-igraph@2.2.1 r-irlba@2.3.5.1 r-lmtest@0.9-40 r-matrix@1.7-4 r-mclust@6.1.2 r-pracma@2.4.6 r-raceid@0.3.9 r-rarpack@0.11-0 r-reticulate@1.44.1 r-robustrankaggreg@1.2.1 r-rsvd@1.0.5 r-seurat@5.3.1 python-anndata@0.12.1 python-geosketch@1.2 python-scanpy@1.11.2 scvelo@0.2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/WWXkenmo/NetID_package
Licenses: Expat
Build system: r
Synopsis: Scalable method to infer fate-specific networks from single-cell data
Description:

This package provides a method to sample cells from single-cell data. It also generates an aggregate profile on a pruned K-Nearest Neighbor graph. This approach leads to an improved gene expression profile for quantifying gene regulations.

muscle 3.8.1551
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://www.drive5.com/muscle
Licenses: Public Domain
Build system: gnu
Synopsis: Multiple sequence alignment program
Description:

MUSCLE aims to be a fast and accurate multiple sequence alignment program for nucleotide and protein sequences.

Page: 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699700701702703704705706707708709710711712713714715716717718719720721722723724725726727728729730731732733734735736737738739740741742743744745746747748749750751752753754755756757758759760761762763764765766767768769770771772773774775776777778779780781782783784785786787788789790791792793794795796797798799800801802803804805806807808809810811812813814815816817818819820821822823824825826827828829830831832833834835836837838839840841842843844845846847848849850851852853854855856857858859860861862863864865866867868869870871872873874875876877878879880881882883884885886887888889890891892893894895896897898899900901902903904905906907908909910911912913914915916917918919920921922923924925926927928929930931932933934935936937938939940941942943944945946947948949950951952953954955956957958959960961962963964965966967968969970971972973974975976977978979980981982983984985986987988989990991992993994995996997998999100010011002100310041005100610071008100910101011101210131014101510161017101810191020102110221023102410251026102710281029103010311032103310341035103610371038103910401041104210431044104510461047104810491050105110521053105410551056105710581059106010611062106310641065106610671068106910701071107210731074107510761077107810791080108110821083108410851086108710881089109010911092109310941095109610971098109911001101110211031104110511061107110811091110111111121113111411151116111711181119112011211122112311241125112611271128112911301131113211331134113511361137113811391140114111421143114411451146114711481149115011511152115311541155115611571158115911601161116211631164116511661167116811691170117111721173117411751176117711781179118011811182118311841185118611871188118911901191119211931194119511961197119811991200120112021203120412051206120712081209121012111212121312141215121612171218121912201221122212231224122512261227122812291230123112321233123412351236123712381239124012411242124312441245124612471248124912501251125212531254125512561257125812591260126112621263126412651266126712681269127012711272127312741275127612771278127912801281128212831284128512861287128812891290129112921293129412951296
Total results: 31087