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

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.


r-scseqcomm 0-0.01076e7
Dependencies: r-add2ggplot@0.3.0 r-chorddiag@0.1.3 r-doparallel@1.0.17 r-dplyr@1.1.4 r-foreach@1.5.2 r-gridextra@2.3 r-ggplot2@4.0.1 r-gtable@0.3.6 r-htmlwidgets@1.6.4 r-igraph@2.2.1 r-matrix@1.7-4 r-org-hs-eg-db@3.22.0 r-psych@2.5.6 r-rcolorbrewer@1.1-3 r-rlang@1.1.6 r-scico@1.5.0 r-tidygraph@1.3.1 r-topgo@2.62.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://gitlab.com/sysbiobig/scseqcomm
Licenses: GPL 3
Build system: r
Synopsis: Inter- and intra- cellular signaling from single cell RNA-seq
Description:

This package is tools for analysing intercellular and intracellular signaling from single cell RNA-seq (scRNA-seq) data.

cpat 3.0.4
Dependencies: r-minimal@4.5.2
Propagated dependencies: python-numpy@1.26.4 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://wlcb.oit.uci.edu/cpat/
Licenses: GPL 2+
Build system: pyproject
Synopsis: Alignment-free distinction between coding and noncoding RNA
Description:

CPAT is a method to distinguish coding and noncoding RNA by using a logistic regression model based on four pure sequence-based, linguistic features: ORF size, ORF coverage, Ficket TESTCODE, and Hexamer usage bias. Linguistic features based method does not require other genomes or protein databases to perform alignment and is more robust. Because it is alignment-free, it runs much faster and also easier to use.

r-domultibarheatmap 0.1.0-1.9e65afa
Propagated dependencies: r-ggplot2@4.0.1 r-magrittr@2.0.4 r-rlang@1.1.6 r-seurat@5.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/elliefewings/DoMultiBarHeatmap
Licenses: CC0
Build system: r
Synopsis: Produce heatmap from a Seurat object with multiple annotation bars
Description:

This package builds on Seurat's Doheatmap function code to produce a heatmap from a Seurat object with multiple annotation bars.

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.

r-codeandroll2 2.3.6-1.d58e258
Propagated dependencies: r-colorramps@2.3.4 r-dplyr@1.1.4 r-gplots@3.2.0 r-gtools@3.9.5 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-sessioninfo@1.2.3 r-sm@2.2-6.0 r-stringendo@0.6.0-1.15594b1 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/CodeAndRoll2
Licenses: GPL 3
Build system: r
Synopsis: CodeAndRoll2 for vector, matrix and list manipulations
Description:

CodeAndRoll2 is a set of more than 130 productivity functions. These functions are used by MarkdownReports, ggExpress, and SeuratUtils.

r-cytobackbone 1.0.0-1.4c1a0a3
Propagated dependencies: r-flowcore@2.22.0 r-flowutils@1.59.0 r-fnn@1.1.4.1 r-ggplot2@4.0.1 r-preprocesscore@1.72.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tchitchek-lab/CytoBackBone
Licenses: GPL 2
Build system: r
Synopsis: Merge phenotype information from different cytometric profiles
Description:

This package implements an algorithm which increases the number of simultaneously measurable markers and in this way helps with study of the immune responses. Thus, the present algorithm, named CytoBackBone, allows combining phenotypic information of cells from different cytometric profiles obtained from different cytometry panels. This computational approach is based on the principle that each cell has its own phenotypic and functional characteristics that can be used as an identification card. CytoBackBone uses a set of predefined markers, that we call the backbone, to define this identification card. The phenotypic information of cells with similar identification cards in the different cytometric profiles is then merged.

python-goatools 1.3.1
Propagated dependencies: python-docopt@0.6.2 python-numpy@1.26.4 python-openpyxl@3.1.5 python-pandas@2.2.3 python-pydot@4.0.1 python-requests@2.32.5 python-scipy@1.12.0 python-setuptools@80.9.0 python-statsmodels@0.14.4 python-xlsxwriter@3.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanghaibao/goatools
Licenses: FreeBSD
Build system: pyproject
Synopsis: Python scripts to find enrichment of GO terms
Description:

Python scripts to find enrichment of GO terms. In addition, this package is used for processing the obo-formatted file from Gene Ontology website. The data structure is a directed acyclic graph that allows easy traversal from leaf to root.

bamtools 2.5.2
Dependencies: jsoncpp@1.9.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pezmaster31/bamtools
Licenses: Expat
Build system: cmake
Synopsis: C++ API and command-line toolkit for working with BAM data
Description:

BamTools provides both a C++ API and a command-line toolkit for handling BAM files.

codingquarry 2.0
Dependencies: openmpi@4.1.6 python2@2.7.18
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/codingquarry/
Licenses: GPL 3+
Build system: gnu
Synopsis: Fungal gene predictor
Description:

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.

intervaltree 0.0.0-1.b90527f
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/intervaltree
Licenses: Expat
Build system: gnu
Synopsis: Minimal C++ interval tree implementation
Description:

An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.

python-genomic-regions 0.0.10
Propagated dependencies: python-future@1.0.0 python-intervaltree@3.1.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pybedtools@0.10.0 python-pybigwig@0.3.22 python-pytest@8.4.1 python-msgpack-numpy@0.4.8 python-cython@3.1.2 python-msgpack@1.1.1 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pypi.org/project/genomic-regions/
Licenses: Expat
Build system: pyproject
Synopsis: Consistently handle genomic regions
Description:

This package aims to simplify working with genomic region / interval data by providing a common interface that lets you access a wide selection of file types and formats for handling genomic region data---all using the same syntax.

roary 3.12.0
Dependencies: bash-minimal@5.2.37 perl-array-utils@0.5 bioperl-minimal@1.7.0 perl-digest-md5-file@0.08 perl-exception-class@1.44 perl-file-find-rule@0.35 perl-file-grep@0.02 perl-file-slurper@0.012 perl-file-which@1.23 perl-graph@0.9704 perl-graph-readwrite@2.09 perl-log-log4perl@1.54 perl-moose@2.2015 perl-perlio-utf8-strict@0.007 perl-text-csv@2.00 bedtools@2.31.1 cd-hit@4.8.1 blast+@2.17.0 mcl@14.137 parallel@20251122 prank@170427 mafft@7.475 fasttree@2.1.10 grep@3.11 sed@4.9 gawk@5.3.0 r-minimal@4.5.2 r-ggplot2@4.0.1 coreutils@9.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sanger-pathogens.github.io/Roary/
Licenses: GPL 3
Build system: perl
Synopsis: High speed stand-alone pan genome pipeline
Description:

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by the Prokka program) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. Roary is not intended for metagenomics or for comparing extremely diverse sets of genomes.

r-stacas 2.2.0
Propagated dependencies: r-biocneighbors@2.4.0 r-biocparallel@1.44.0 r-ggplot2@4.0.1 r-ggridges@0.5.7 r-pbapply@1.7-4 r-r-utils@2.13.0 r-seurat@5.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/carmonalab/STACAS
Licenses: GPL 3
Build system: r
Synopsis: Sub-type anchoring correction for alignment in Seurat
Description:

This package implements methods for batch correction and integration of scRNA-seq datasets, based on the Seurat anchor-based integration framework. In particular, STACAS is optimized for the integration of heterogeneous datasets with only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods would tend to over-correct biological differences. The 2.0 version of the package allows the users to incorporate explicit information about cell-types in order to assist the integration process.

r-chipkernels 1.1-1.c9cfcac
Propagated dependencies: r-iranges@2.44.0 r-xvector@0.50.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-gtools@3.9.5 r-genomicranges@1.62.0 r-sfsmisc@1.1-23 r-kernlab@0.9-33 r-s4vectors@0.48.0 r-biocgenerics@0.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ManuSetty/ChIPKernels
Licenses: GPL 2+
Build system: r
Synopsis: Build string kernels for DNA Sequence analysis
Description:

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

miniasm 0.3
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lh3/miniasm
Licenses: Expat
Build system: gnu
Synopsis: Ultrafast de novo assembly for long noisy reads
Description:

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.

ngless 1.5.0
Dependencies: bash-minimal@5.2.37 prodigal@2.6.3 bwa@0.7.18 samtools@1.19 minimap2@2.28 megahit@1.2.9 ghc-missingh@1.5.0.1 ghc-aeson@2.0.3.0 ghc-ansi-terminal@0.11.4 ghc-async@2.2.4 ghc-atomic-write@0.2.0.7 ghc-bytestring-lexing@0.5.0.10 ghc-conduit@1.3.5 ghc-conduit-algorithms@0.0.13.0 ghc-conduit-extra@1.3.6 ghc-configurator@0.3.0.0 ghc-convertible@1.1.1.1 ghc-data-default@0.7.1.1 ghc-edit-distance@0.2.2.1 ghc-either@5.0.2 ghc-errors@2.3.0 ghc-extra@1.7.13 ghc-file-embed@0.0.15.0 ghc-filemanip@0.3.6.3 ghc-hashable@1.4.2.0 ghc-hashtables@1.3.1 ghc-hostname@1.0 ghc-http-client@0.7.13.1 ghc-http-conduit@2.3.8.1 ghc-inline-c@0.9.1.8 ghc-inline-c-cpp@0.5.0.0 ghc-int-interval-map@0.0.0.0 ghc-network@3.1.4.0 ghc-optparse-applicative@0.17.1.0 ghc-primitive@0.7.3.0 ghc-random-shuffle@0.0.4 ghc-regex@1.1.0.2 ghc-resourcet@1.2.6 ghc-safe@0.3.19 ghc-stm-chans@3.0.0.9 ghc-stm-conduit@4.0.1 ghc-strict@0.4.0.1 ghc-tar@0.5.1.1 ghc-tar-conduit@0.3.2 ghc-unix-compat@0.5.4 ghc-unliftio@0.2.25.0 ghc-unliftio-core@0.2.1.0 ghc-vector@0.12.3.1 ghc-vector-algorithms@0.8.0.4 ghc-yaml@0.11.11.1 ghc-zlib@0.6.3.0 ghc-bzlib-conduit@0.3.0.2 ghc-double-conversion@2.0.4.2 ghc-safeio@0.0.5.0
Propagated dependencies: r-r6@2.6.1 r-hdf5r@1.3.12 r-iterators@1.0.14 r-itertools@0.1-3 r-matrix@1.7-4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ngless.embl.de/
Licenses: Expat
Build system: haskell
Synopsis: DSL for processing next-generation sequencing data
Description:

Ngless is a domain-specific language for next-generation sequencing (NGS) data processing.

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.

java-htsjdk 2.10.1
Dependencies: java-ngs@2.10.5 java-snappy@1.0.3-rc3 java-commons-compress@1.21 java-commons-logging-minimal@1.2 java-commons-jexl@2.1.1 java-xz@1.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.github.io/htsjdk/
Licenses: Expat
Build system: ant
Synopsis: Java API for high-throughput sequencing data (HTS) formats
Description:

HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.

python-bamnostic 1.1.8
Propagated dependencies: python-pytest@8.4.1 python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/betteridiot/bamnostic/
Licenses: Modified BSD
Build system: pyproject
Synopsis: Tool for binary alignment map, random access and parsing
Description:

Bamnostic is a pure Python Binary Alignment Map (BAM) file parser and random access tool.

python-biopython 1.85
Propagated dependencies: python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biopython.org/
Licenses: non-copyleft
Build system: pyproject
Synopsis: Tools for biological computation in Python
Description:

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

kallisto 0.50.1
Dependencies: hdf5@1.14.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pachterlab.github.io/kallisto/
Licenses: FreeBSD
Build system: cmake
Synopsis: Near-optimal RNA-Seq quantification
Description:

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.

python-pybbi 0.4.1
Dependencies: libpng@1.6.39 openssl@3.0.8 zlib@1.3.1
Propagated dependencies: python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nvictus/pybbi
Licenses: Expat
Build system: pyproject
Synopsis: Python bindings to UCSC Big Binary file library
Description:

This package provides Python bindings to the UCSC Big Binary (bigWig/bigBed) file library. This provides read-level access to local and remote bigWig and bigBed files but no write capabilitites. The main feature is fast retrieval of range queries into numpy arrays.

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