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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.


python-hic2cool 1.0.1
Propagated dependencies: python-cooler@0.9.3 python-h5py@3.13.0 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://github.com/4dn-dcic/hic2cool
Licenses: Expat
Build system: pyproject
Synopsis: Converter for .hic and .cool files
Description:

This package provides a converter between .hic files (from juicer) and single-resolution or multi-resolution .cool files (for cooler). Both hic and cool files describe Hi-C contact matrices.

python-loompy 3.0.7
Propagated dependencies: python-click@8.1.8 python-h5py@3.13.0 python-numba@0.61.0 python-numpy@1.26.4 python-numpy-groupies@0.11.3 python-pandas@2.2.3 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/linnarsson-lab/loompy
Licenses: Modified BSD
Build system: pyproject
Synopsis: Work with .loom files for single-cell RNA-seq data
Description:

The loom file format is an efficient format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations. Loom also supports sparse graphs. This library makes it easy to work with .loom files for single-cell RNA-seq data.

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-copykat 1.0.8-0.256de33
Propagated dependencies: r-cluster@2.1.8.1 r-dlm@1.1-6.1 r-gplots@3.2.0 r-mcmcpack@1.7-1 r-mixtools@2.0.0.1 r-paralleldist@0.2.7 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/navinlabcode/copykat
Licenses: GPL 2
Build system: r
Synopsis: Inference of genomic copy number from single cell RNAseq data
Description:

This package Copynumber KAryotyping of Tumors infers genomic copy number and subclonal structure of human tumors using integrative Bayesian approaches to identify genome-wide aneuploidy at 5MB resolution in single cells data. It separates tumor cells and tumor subclones from normal cells using high-throughput sc-RNAseq data.

sailfish 0.10.1
Dependencies: boost@1.83.0 eigen@3.4.0 jemalloc@5.3.0 jellyfish@2.3.0 sparsehash@2.0.4 libdivsufsort@2.0.1 libgff@2.0.0 tbb@2020.3 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.cs.cmu.edu/~ckingsf/software/sailfish/
Licenses: GPL 3+
Build system: cmake
Synopsis: Mapping-based isoform quantification from RNA-Seq reads
Description:

Sailfish is a tool for genomic transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run sailfish is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your reads.

r-databaselinke-r 1.7.0-1.cf3d6cc
Propagated dependencies: r-readwriter@1.5.3-1.91373c4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/DatabaseLinke.R
Licenses: GPL 3
Build system: r
Synopsis: Parse links to databases from your list of gene symbols
Description:

This package provides a set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

python-pyega3 5.2.1
Propagated dependencies: python-htsget@0.2.6 python-psutil@7.0.0 python-requests@2.32.5 python-tqdm@4.67.1 python-urllib3@2.5.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/EGA-archive/ega-download-client
Licenses: ASL 2.0
Build system: pyproject
Synopsis: EGA download client
Description:

PyEGA3 is a tool for viewing and downloading files from authorized EGA datasets. It uses the EGA data API and has several key features:

  • Files are transferred over secure https connections and received unencrypted, so no need for decryption after download.

  • Downloads resume from where they left off in the event that the connection is interrupted.

  • Supports file segmenting and parallelized download of segments, improving overall performance.

  • After download completes, file integrity is verified using checksums.

  • Implements the GA4GH-compliant htsget protocol for download of genomic ranges for data files with accompanying index files.

prodigal 2.6.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hyattpd/Prodigal
Licenses: GPL 3+
Build system: gnu
Synopsis: Protein-coding gene prediction for Archaea and Bacteria
Description:

Prodigal runs smoothly on finished genomes, draft genomes, and metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table format. It runs quickly, in an unsupervised fashion, handles gaps, handles partial genes, and identifies translation initiation sites.

mafft 7.475
Dependencies: bash-minimal@5.2.37 perl@5.36.0 ruby@3.3.9 gawk@5.3.0 grep@3.11 coreutils@9.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://mafft.cbrc.jp/alignment/software/
Licenses: non-copyleft
Build system: gnu
Synopsis: Multiple sequence alignment program
Description:

MAFFT offers a range of multiple alignment methods for nucleotide and protein sequences. For instance, it offers L-INS-i (accurate; for alignment of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 sequences).

libgff 2.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/COMBINE-lab/libgff
Licenses: X11-style
Build system: cmake
Synopsis: Parser library for reading/writing GFF files
Description:

This is a simple "libraryfication" of the GFF/GTF parsing code that is used in the Cufflinks codebase. The goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.

r-scent 1.0.0-1.f01f18a
Dependencies: bedtools@2.31.1
Propagated dependencies: r-boot@1.3-32 r-data-table@1.17.8 r-hmisc@5.2-4 r-lme4@1.1-37 r-mass@7.3-65 r-matrix@1.7-4 r-r-utils@2.13.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/immunogenomics/SCENT
Licenses: Expat
Build system: r
Synopsis: Single-Cell enhancer target gene mapping for multimodal single-cell data
Description:

This package contains functions for the SCENT algorithm. SCENT uses single-cell multimodal data and links ATAC-seq peaks to their target genes by modeling association between chromatin accessibility and gene expression across individual single cells.

bpp-seq-omics 2.4.1
Dependencies: bpp-core@2.4.1 bpp-seq@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BioPP/bpp-seq-omics
Licenses: CeCILL
Build system: cmake
Synopsis: Bio++ sequence library genomics components
Description:

This library contains the genomics components of the Bio++ sequence library. It is part of the Bio++ project.

fastahack 1.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/fastahack
Licenses: Expat GPL 2
Build system: gnu
Synopsis: Indexing and sequence extraction from FASTA files
Description:

Fastahack is a small application for indexing and extracting sequences and subsequences from FASTA files. The included library provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.

trf 4.09.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Benson-Genomics-Lab/TRF
Licenses: AGPL 3+
Build system: gnu
Synopsis: Tandem Repeats Finder: a program to analyze DNA sequences
Description:

A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. The output consists of two files: a repeat table file and an alignment file. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected.

python-pygenometracks 3.5
Propagated dependencies: python-future@1.0.0 python-gffutils@0.13 python-hicmatrix@17.1 python-intervaltree@3.1.0 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pybigwig@0.3.22 python-pysam@0.23.0 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pygenometracks.readthedocs.io
Licenses: GPL 3+
Build system: pyproject
Synopsis: Program and library to plot beautiful genome browser tracks
Description:

This package aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig, bed (many options), bedgraph, links (represented as arcs), and Hi-C matrices. pyGenomeTracks can make plots with or without Hi-C data.

macs 2.2.9.1
Propagated dependencies: python-cython@0.29.37 python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/macs3-project/MACS
Licenses: Modified BSD
Build system: pyproject
Synopsis: Model based analysis for ChIP-Seq data
Description:

MACS is an implementation of a ChIP-Seq analysis algorithm for identifying transcript factor binding sites named Model-based Analysis of ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and it improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

tombo 1.5.1
Propagated dependencies: python-future@1.0.0 python-h5py@3.13.0 python-mappy@2.24 python-numpy@1.26.4 python-scipy@1.12.0 python-tqdm@4.67.1 python-rpy2@3.5.17
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nanoporetech/tombo
Licenses: MPL 2.0
Build system: pyproject
Synopsis: Analysis of raw nanopore sequencing data
Description:

Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. Tombo also provides tools for the analysis and visualization of raw nanopore signal.

newick-utils 1.6-1.da121155
Dependencies: libxml2@2.14.6 flex@2.6.4 bison@3.8.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tjunier/newick_utils
Licenses: Modified BSD
Build system: gnu
Synopsis: Programs for working with newick format phylogenetic trees
Description:

Newick-utils is a suite of utilities for processing phylogenetic trees in Newick format. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).

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.

dropseq-tools 1.13
Dependencies: icedtea@3.19.0 java-picard@2.10.3 java-log4j-1.2-api@2.17.1 java-commons-math3@3.6.1 java-commons-jexl@2.1.1 java-commons-collections4@4.1 java-commons-lang@2.6 java-commons-io@2.5 java-snappy@1.0.3-rc3 java-guava@31.1 java-la4j@0.6.0 java-biojava-core@4.0.0 java-biojava-alignment@4.0.0 java-jdistlib@0.4.5 java-simple-xml@2.7.1 java-snakeyaml@1.18
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://mccarrolllab.com/dropseq/
Licenses: Expat
Build system: ant
Synopsis: Tools for Drop-seq analyses
Description:

Drop-seq is a technology to enable biologists to analyze RNA expression genome-wide in thousands of individual cells at once. This package provides tools to perform Drop-seq analyses.

stringtie 3.0.2
Dependencies: bzip2@1.0.8 htslib@1.21 libdeflate@1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ccb.jhu.edu/software/stringtie/
Licenses: Expat
Build system: gnu
Synopsis: Transcript assembly and quantification for RNA-Seq data
Description:

StringTie is a fast and efficient assembler of RNA-Seq sequence alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

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.

scregseg 0.1.3-0.78ebff8
Propagated dependencies: python-scikit-learn@1.6.1 python-scipy@1.12.0 python-numpy@1.26.4 python-hmmlearn@0.3.3 python-pandas@2.2.3 python-numba@0.61.0 python-anndata@0.12.1 python-scanpy@1.11.2 python-pybedtools@0.10.0 python-pysam@0.23.0 python-matplotlib@3.8.2 python-seaborn@0.13.2 python-coolbox@0.3.8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/scregseg
Licenses: GPL 3+
Build system: pyproject
Synopsis: Single-cell regulatory landscape segmentation
Description:

Scregseg (Single-Cell REGulatory landscape SEGmentation) is a tool that facilitates the analysis of single cell ATAC-seq data by an HMM-based segmentation algorithm. Scregseg uses an HMM with Dirichlet-Multinomial emission probabilities to segment the genome either according to distinct relative cross-cell accessibility profiles or (after collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct cross-cluster accessibility profiles.

java-picard 2.3.0
Dependencies: java-htsjdk@2.3.0 java-guava@31.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://broadinstitute.github.io/picard/
Licenses: Expat
Build system: ant
Synopsis: Tools for manipulating high-throughput sequencing data and formats
Description:

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.

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