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

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.


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.

express-beta-diversity 1.0.8
Dependencies: python2@2.7.18
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dparks1134/ExpressBetaDiversity
Licenses: GPL 3+
Build system: gnu
Synopsis: Taxon- and phylogenetic-based beta diversity measures
Description:

Express Beta Diversity (EBD) calculates ecological beta diversity (dissimilarity) measures between biological communities. EBD implements a variety of diversity measures including those that make use of phylogenetic similarity of community members.

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-cwl-upgrader 1.2.11
Propagated dependencies: python-ruamel.yaml@0.18.14 python-schema-salad@8.9.20250723145140
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/common-workflow-language/cwl-upgrader
Licenses: ASL 2.0
Build system: pyproject
Synopsis: CWL document upgrader
Description:

python-cwl-upgrader is a standalone upgrader for CWL documents from version draft-3, v1.0, and v1.1 to v1.2.

python-magic-impute 1.2.1
Propagated dependencies: python-future@1.0.0 python-graphtools@1.5.3 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-tasklogger@1.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/KrishnaswamyLab/MAGIC
Licenses: GPL 2+
Build system: pyproject
Synopsis: Markov affinity-based graph imputation of cells
Description:

MAGIC is an interactive tool to impute missing values in single-cell sequencing data and to restore the structure of the data. It also provides data pre-processing functionality such as dimensionality reduction and gene expression visualization.

python-pdbfixer 1.9
Propagated dependencies: openmm@8.3.1 python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/openmm/pdbfixer
Licenses: Expat
Build system: pyproject
Synopsis: Application for fixing problems in Protein Data Bank
Description:

PDBFixer is designed to rectify issues in Protein Data Bank files. Its intuitive interface simplifies the process of resolving problems encountered in PDB files prior to simulation tasks.

bedtools 2.18.0
Dependencies: samtools@1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/arq5x/bedtools2
Licenses: Expat
Build system: gnu
Synopsis: Tools for genome analysis and arithmetic
Description:

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

r-gutils 0.2.0-2.fc24db6
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrix@1.7-4 r-s4vectors@0.48.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/gUtils
Licenses: GPL 2
Build system: r
Synopsis: Additional capabilities and speed for GenomicRanges operations
Description:

This is an R package providing additional capabilities and speed for GenomicRanges operations.

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-ggexpress 0.6.6-1.82f1693
Propagated dependencies: r-cowplot@1.2.0 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-markdownhelpers@0.2.0-1.793372d r-markdownreports@4.5.9-1.3ba1103 r-rcolorbrewer@1.1-3 r-sessioninfo@1.2.3 r-seurat@5.3.1 r-sm@2.2-6.0 r-stringendo@0.6.0-1.15594b1 r-tidyverse@2.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/ggExpress
Licenses: GPL 3
Build system: r
Synopsis: This is a fast tool to create, annotate and export plots in R
Description:

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

r-umi4cpackage 0.0.1-1.88b07d8
Dependencies: perl@5.36.0 bowtie@2.3.4.3
Propagated dependencies: r-misha@4.1.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanaylab/umi4cpackage
Licenses: Expat
Build system: r
Synopsis: Processing and analysis of UMI-4C contact profiles
Description:

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

r-premessa 0.3.4-1.68b42bb
Propagated dependencies: r-data-table@1.17.8 r-flowcore@2.22.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-hexbin@1.28.5 r-jsonlite@2.0.0 r-reshape@0.8.10 r-rhandsontable@0.3.8 r-shiny@1.11.1 r-shinyjqui@0.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ParkerICI/premessa
Licenses: GPL 3
Build system: r
Synopsis: Pre-processing of flow and mass cytometry data
Description:

This is an R package for pre-processing of flow and mass cytometry data. This package includes panel editing or renaming for FCS files, bead-based normalization and debarcoding.

python-pygam 0.9.1
Propagated dependencies: python-black@25.1.0 python-flake8@7.1.1 python-ipython@8.37.0 python-numpy@1.26.4 python-pandas@2.2.3 python-poetry-core@2.1.3 python-progressbar2@4.5.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dswah/pyGAM
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Generalized additive models in Python
Description:

This tool is for building Generalized Additive Models in Python. It emphasizes modularity and performance. The API will be immediately familiar to anyone with experience of scikit-learn or scipy.

python-bed-reader 1.0.6
Dependencies: python-wrapper@3.11.14 rust-ring@0.17.8
Propagated dependencies: python-numpy@1.26.4 python-pandas@2.2.3 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://fastlmm.github.io/
Licenses: ASL 2.0
Build system: cargo
Synopsis: Read and write the PLINK BED format, simply and efficiently
Description:

This package lets you read and write the PLINK BED format, simply and efficiently.

r-sleuth 0.30.1
Propagated dependencies: r-aggregation@1.0.1 r-data-table@1.17.8 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-lazyeval@0.2.2 r-matrixstats@1.5.0 r-pheatmap@1.0.13 r-reshape2@1.4.5 r-rhdf5@2.54.0 r-shiny@1.11.1 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pachterlab/sleuth
Licenses: GPL 3
Build system: r
Synopsis: Tools for investigating RNA-Seq
Description:

Sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via Kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.

r-singlet 0.99.26-1.765a6c4
Propagated dependencies: r-dplyr@1.1.4 r-fgsea@1.36.0 r-ggplot2@4.0.1 r-knitr@1.50 r-limma@3.66.0 r-matrix@1.7-4 r-msigdbr@25.1.1 r-rcpp@1.1.0 r-rcppml-devel@0.5.6-2.5449a5b r-reshape2@1.4.5 r-scuttle@1.20.0 r-seurat@5.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/zdebruine/singlet
Licenses: GPL 2+
Build system: r
Synopsis: Non-negative Matrix Factorization for single-cell analysis
Description:

This is a package for fast Non-negative Matrix Factorization (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.

bpp-seq 2.4.1
Dependencies: bpp-core@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pbil.univ-lyon1.fr/bpp-doc/bpp-seq/html/
Licenses: CeCILL-C
Build system: cmake
Synopsis: Bio++ sequence library
Description:

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides sequence-related modules.

r-scopeloomr 0.13.0-1.99726f5
Propagated dependencies: r-base64enc@0.1-3 r-hdf5r@1.3.12 r-igraph@2.2.1 r-matrix@1.7-4 r-plyr@1.8.9 r-rjson@0.2.23 r-rlist@0.4.6.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aertslab/SCopeLoomR
Licenses: Expat
Build system: r
Synopsis: Build .loom files and extract data from them
Description:

This is an R package to build generic .loom files aligning with the default naming convention of the .loom format and to integrate other data types e.g.: regulons (SCENIC), clusters from Seurat, trajectory information... The package can also be used to extract data from .loom files.

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

savvy 2.1.0
Dependencies: htslib@1.21
Propagated dependencies: streambuf-shrinkwrap@1.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/statgen/savvy/
Licenses: MPL 2.0
Build system: cmake
Synopsis: Interface to various variant calling formats
Description:

Savvy is the official C++ interface for the SAV file format and offers seamless support for BCF and VCF files.

louvain 0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/louvain/
Licenses: GPL 3+
Build system: gnu
Synopsis: Multi-criteria community detection
Description:

This package offers a set of functions to use in order to compute communities on graphs weighted or unweighted.

r-presto 1.0.0-1.7636b3d
Propagated dependencies: r-data-table@1.17.8 r-dplyr@1.1.4 r-matrix@1.7-4 r-purrr@1.2.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rlang@1.1.6 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/immunogenomics/presto
Licenses: GPL 3
Build system: r
Synopsis: Fast Functions for Differential Expression using Wilcox and AUC
Description:

This package performs a fast Wilcoxon rank sum test and auROC analysis.

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.

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Total results: 69112