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

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.


subread 2.0.3
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://subread.sourceforge.net/
Licenses: GPL 3+
Build system: gnu
Synopsis: Tool kit for processing next-gen sequencing data
Description:

The subread package contains the following tools: subread aligner, a general-purpose read aligner; subjunc aligner: detecting exon-exon junctions and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic features; exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

python-pyvcf3 1.0.3-0.1fb3789
Propagated dependencies: python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dridk/PyVCF3
Licenses: Expat
Build system: pyproject
Synopsis: Variant Call Format parser for Python
Description:

This package provides a VCF parser for Python.

r-rhtslib12 1.23.2-1.ee186da
Propagated dependencies: curl@8.6.0 zlib@1.3.1 r-zlibbioc@1.54.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haizi-zh/Rhtslib12
Licenses: LGPL 2.0+
Build system: r
Synopsis: HTSlib high-throughput sequencing library as an R package
Description:

This package provides version 1.12 of the HTSlib C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.

minced 0.3.2
Dependencies: bash@5.2.37 icedtea@3.19.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ctSkennerton/minced
Licenses: GPL 3+
Build system: gnu
Synopsis: Mining CRISPRs in Environmental Datasets
Description:

MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for unassembled metagenomic reads, but is mainly designed for full genomes and assembled metagenomic sequence.

python-bcbio-gff 0.7.1
Propagated dependencies: python-biopython@1.85 python-six@1.17.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/chapmanb/bcbb/tree/master/gff
Licenses: non-copyleft
Build system: pyproject
Synopsis: Read and write GFF files with Biopython integration
Description:

This package lets you read and write files in Generic Feature Format (GFF) with Biopython integration.

vcftools 0.1.16
Dependencies: perl@5.36.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://vcftools.github.io/
Licenses: LGPL 3
Build system: gnu
Synopsis: Tools for working with VCF files
Description:

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

delly 0.8.3
Dependencies: boost@1.89.0 bzip2@1.0.8 htslib@1.21 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dellytools/delly
Licenses: GPL 3+
Build system: gnu
Synopsis: Integrated structural variant prediction method
Description:

Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

samtools 0.1.19
Dependencies: htslib@1.21 ncurses@6.2.20210619 perl@5.36.0 python@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.sourceforge.net
Licenses: Expat
Build system: gnu
Synopsis: Utilities to efficiently manipulate nucleotide sequence alignments
Description:

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

r-icellnet 2.2.1-1.e10ee4a
Propagated dependencies: r-annotationdbi@1.72.0 r-complexheatmap@2.26.0 r-circlize@0.4.16 r-data-table@1.17.8 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-hgu133plus2-db@3.13.0 r-jetset@3.4.0 r-psych@2.5.6 r-reshape2@1.4.5 r-rlist@0.4.6.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/soumelis-lab/ICELLNET
Licenses: GPL 3
Build system: r
Synopsis: Transcriptomic-based framework to dissect cell communication
Description:

This package provides a a transcriptomic-based framework to dissect cell communication in a global manner. It integrates an original expert-curated database of ligand-receptor interactions taking into account multiple subunits expression. Based on transcriptomic profiles (gene expression), this package computes communication scores between cells and provides several visualization modes that can be helpful to dig into cell-cell interaction mechanism and extend biological knowledge.

segemehl 0.3.4
Dependencies: htslib@1.21 ncurses@6.2.20210619 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinf.uni-leipzig.de/Software/segemehl
Licenses: GPL 3+
Build system: gnu
Synopsis: Map short sequencer reads to reference genomes
Description:

Segemehl is software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file.

python-multivelo 0.1.2
Propagated dependencies: python-anndata@0.12.1 python-h5py@3.13.0 python-ipywidgets@8.1.2 python-joblib@1.5.2 python-loompy@3.0.7 python-matplotlib@3.8.2 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-tqdm@4.67.1 python-umap-learn@0.5.9 scvelo@0.2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/welch-lab/MultiVelo
Licenses: Modified BSD
Build system: pyproject
Synopsis: Velocity inference from single-cell multi-omic data
Description:

MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of gene regulation, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes.

python-bulkvis 2.0.0-2.00a82a9
Propagated dependencies: python-bokeh@3.7.3 python-dill@0.4.0 python-h5py@3.13.0 python-joblib@1.5.2 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-plotly@5.20.0 python-readpaf@0.0.10 python-scikit-learn@1.7.0 python-scikit-image@0.23.2 python-scipy@1.12.0 python-seaborn@0.13.2 python-tornado@6.4.2 python-tqdm@4.67.1 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/LooseLab/bulkVis
Licenses: Expat
Build system: pyproject
Synopsis: Interactive visualization of bulk RNA-seq data
Description:

This is a Python package for the interactive visualization of bulk RNA-seq data. It provides a range of plotting functions and interactive tools to explore and analyze bulk RNA-seq data.

shorah 1.99.2
Dependencies: bash-minimal@5.2.37 boost@1.89.0 htslib@1.21 python@3.11.14 python-biopython@1.85 python-numpy@1.26.4 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page:
Licenses: GPL 3+
Build system: gnu
Synopsis: Short reads assembly into haplotypes
Description:

ShoRAH is a project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

ngs-sdk 2.10.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ncbi/ngs
Licenses: Public Domain
Build system: gnu
Synopsis: API for accessing Next Generation Sequencing data
Description:

NGS is a domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously.

python-mappy 2.24
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lh3/minimap2
Licenses: Expat
Build system: pyproject
Synopsis: Python binding for minimap2
Description:

This package provides a convenient interface to minimap2, a fast and accurate C program to align genomic and transcribe nucleotide sequences.

scvelo 0.2.4
Propagated dependencies: pybind11@2.13.6 python-anndata@0.12.1 python-hnswlib@0.5.2 python-igraph@0.11.8 python-loompy@3.0.7 python-louvain@0.16 python-matplotlib@3.8.2 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://scvelo.org
Licenses: Modified BSD
Build system: pyproject
Synopsis: RNA velocity generalized through dynamical modeling
Description:

ScVelo is a scalable toolkit for RNA velocity analysis in single cells. RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. scVelo generalizes the concept of RNA velocity by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.

pigx-rnaseq 0.1.1
Dependencies: coreutils@9.1 sed@4.9 gzip@1.14 snakemake@7.32.4 megadepth@1.1.1 multiqc@1.14 star@2.7.3a hisat2@2.2.1 fastp@0.23.2 htseq@2.0.2 samtools@1.19 r-minimal@4.5.2 r-rmarkdown@2.30 r-genomeinfodb@1.46.0 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-ggrepel@0.9.6 r-gprofiler2@0.2.4 r-deseq2@1.50.2 r-dt@0.34.0 r-knitr@1.50 r-pheatmap@1.0.13 r-corrplot@0.95 r-reshape2@1.4.5 r-plotly@4.11.0 r-scales@1.4.0 r-summarizedexperiment@1.40.0 r-crosstalk@1.2.2 r-tximport@1.38.1 r-rtracklayer@1.70.0 r-rjson@0.2.23 salmon@1.10.3 pandoc@2.19.2 python-wrapper@3.11.14 python-deeptools@3.5.5 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinformatics.mdc-berlin.de/pigx/
Licenses: GPL 3+
Build system: gnu
Synopsis: Analysis pipeline for RNA sequencing experiments
Description:

PiGX RNAseq is an analysis pipeline for preprocessing and reporting for RNA sequencing experiments. It is easy to use and produces high quality reports. The inputs are reads files from the sequencing experiment, and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline produces a differential expression report comparing samples in an easily configurable manner.

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.

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.

sjcount 3.2-1.292d391
Dependencies: samtools@0.1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pervouchine/sjcount-full/
Licenses: GPL 3+
Build system: gnu
Synopsis: Annotation-agnostic splice junction counting pipeline
Description:

Sjcount is a utility for fast quantification of splice junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This version does count multisplits.

python-hotspotsc 1.1.1
Propagated dependencies: python-anndata@0.12.1 python-importlib-metadata@8.7.0 python-ipython@8.37.0 python-matplotlib@3.8.2 python-nbsphinx@0.8.8 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pynndescent@0.5.13 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-statsmodels@0.14.4 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/yoseflab/hotspot
Licenses: Expat
Build system: pyproject
Synopsis: Identifying informative genes in a single-cell dataset
Description:

Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Importantly, "informative" is decided based on how well a gene's variation agrees with some cell metric---some similarity mapping between cells. Genes which are informative are those whose expression varies in similar way among cells which are nearby in the given metric.

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.

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