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

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-seuratwrappers 0.3.1-1.d28512f
Propagated dependencies: r-biocmanager@1.30.27 r-cowplot@1.2.0 r-ggplot2@4.0.1 r-igraph@2.2.1 r-matrix@1.7-4 r-remotes@2.5.0 r-rlang@1.1.6 r-rsvd@1.0.5 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/satijalab/seurat-wrappers
Licenses: GPL 3
Build system: r
Synopsis: Community-provided methods and extensions for the Seurat object
Description:

SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently.

raxml 8.2.12
Dependencies: openmpi@4.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://cme.h-its.org/exelixis/web/software/raxml/index.html
Licenses: GPL 2+
Build system: gnu
Synopsis: Randomized Axelerated Maximum Likelihood phylogenetic trees
Description:

RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.

python-logomaker 0.8.7
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jbkinney/logomaker
Licenses: Expat
Build system: pyproject
Synopsis: Package for making Sequence Logos
Description:

Logomaker is a Python package for generating publication-quality sequence logos. Logomaker can generate both standard and highly customized logos illustrating the properties of DNA, RNA, or protein sequences. Logos are rendered as vector graphics embedded within native matplotlib Axes objects, making them easy to style and incorporate into multi-panel figures.

vcflib 1.0.12
Dependencies: bzip2@1.0.8 curl@8.6.0 htslib@1.21 fastahack@1.0.0 perl@5.36.0 python@3.11.14 pybind11@2.13.6 smithwaterman@0.0.0-2.2610e25 tabixpp@1.1.2 xz@5.4.5 zlib@1.3.1
Propagated dependencies: wfa2-lib@2.3.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vcflib/vcflib/
Licenses: Expat
Build system: cmake
Synopsis: Library for parsing and manipulating VCF files
Description:

Vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both an API for parsing and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.

indelfixer 1.1
Dependencies: java-commons-lang@2.6 java-args4j@2.33
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cbg-ethz/InDelFixer/
Licenses: GPL 3+
Build system: ant
Synopsis: Iterative and sensitive NGS sequence aligner
Description:

InDelFixer is a sensitive aligner for 454, Illumina and PacBio data, employing a full Smith-Waterman alignment against a reference. This Java command line application aligns Next-Generation Sequencing (NGS) and third-generation reads to a set of reference sequences, by a prior fast k-mer matching and removes indels, causing frame shifts. In addition, only a specific region can be considered. An iterative refinement of the alignment can be performed, by alignment against the consensus sequence with wobbles. The output is in SAM 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-p2data 1.0.0-1.7d4c0e1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/kharchenkolab/p2data
Licenses: GPL 3
Build system: r
Synopsis: Data for pagoda2
Description:

This package contains data used by pagoda2. The data within this package are the 3000 bone marrow cells used for vignettes.

piranha 1.2.1-1.0466d36
Dependencies: bamtools@2.5.2 samtools@0.1.19 gsl@2.8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/smithlabcode/piranha
Licenses: GPL 3+
Build system: gnu
Synopsis: Peak-caller for CLIP-seq and RIP-seq data
Description:

Piranha is a peak-caller for genomic data produced by CLIP-seq and RIP-seq experiments. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.

java-ngs 2.10.5
Dependencies: icedtea@3.19.0 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: Java bindings for NGS SDK
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.

ataqv 1.0.0
Dependencies: boost@1.83.0 htslib@1.21 ncurses@6.2.20210619 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ParkerLab/ataqv
Licenses: GPL 3+
Build system: gnu
Synopsis: Toolkit for quality control and visualization of ATAC-seq data
Description:

This package provides a toolkit for measuring and comparing ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, ataqv, examines aligned reads and reports some basic metrics.

python-mygene 3.2.2
Propagated dependencies: python-biothings-client@0.2.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biothings/mygene.py
Licenses: Modified BSD
Build system: python
Synopsis: Python Client for MyGene.Info services
Description:

MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. Mygene is a Python wrapper to access MyGene.Info services.

java-forester 0-1.86b07ef
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-cgatcore 0.6.16
Dependencies: time@1.9
Propagated dependencies: python-apsw@3.46.0.0 python-gevent@24.11.1 python-pandas@2.2.3 python-paramiko@4.0.0 python-pyyaml@6.0.2 python-ruffus@2.8.4 python-sqlalchemy@1.4.42
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cgat-developers/cgat-core
Licenses: Expat
Build system: pyproject
Synopsis: Computational genomics analysis toolkit
Description:

CGAT-core is a set of libraries and helper functions used to enable researchers to design and build computational workflows for the analysis of large-scale data-analysis.

bwa-meth 0.2.9
Dependencies: bwa@0.7.18 python-toolshed@0.4.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/brentp/bwa-meth
Licenses: Expat
Build system: pyproject
Synopsis: Fast and accurante alignment of BS-Seq reads
Description:

BWA-Meth works for single-end reads and for paired-end reads from the directional protocol (most common). It uses the method employed by methylcoder and Bismark of in silico conversion of all C's to T's in both reference and reads. It recovers the original read (needed to tabulate methylation) by attaching it as a comment which BWA appends as a tag to the read. It performs favorably to existing aligners gauged by number of on and off-target reads for a capture method that targets CpG-rich region.

python-biopython 1.73
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.

trim-galore 0.6.6
Dependencies: gzip@1.14 perl@5.36.0 pigz@2.8 cutadapt@4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Licenses: GPL 3+
Build system: gnu
Synopsis: Wrapper around Cutadapt and FastQC
Description:

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.

multichoose 1.0.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/multichoose
Licenses: Expat
Build system: gnu
Synopsis: Efficient loopless multiset combination generation algorithm
Description:

This library implements an efficient loopless multiset combination generation algorithm which is (approximately) described in "Loopless algorithms for generating permutations, combinations, and other combinatorial configurations.", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)

r-music 1.0.0-2.f21fe67
Propagated dependencies: r-biobase@2.70.0 r-ggplot2@4.0.1 r-matrix@1.7-4 r-mcmcpack@1.7-1 r-nnls@1.6 r-singlecellexperiment@1.32.0 r-toast@1.24.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/xuranw/MuSiC
Licenses: GPL 3+
Build system: r
Synopsis: Multi-subject single cell deconvolution
Description:

MuSiC is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data.

r-gtrack 0.1.0-1.a694fa3
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gutils@0.2.0-2.fc24db6 r-iranges@2.44.0 r-matrix@1.7-4 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-rcurl@1.98-1.17 r-rtracklayer@1.70.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/gTrack/
Licenses: GPL 2
Build system: r
Synopsis: Plot tracks of complex genomic data across multiple genomic windows
Description:

This package provides an object for plotting GRanges, RleList, UCSC file formats, and ffTrack objects in multi-track panels.

multiqc 1.14
Dependencies: python-click@8.1.8 python-coloredlogs@10.0 python-future@1.0.0 python-jinja2@3.1.2 python-lzstring@1.0.4 python-markdown@3.10 python-matplotlib@3.8.2 python-networkx@3.4.2 python-numpy@1.26.4 python-pyyaml@6.0.2 python-requests@2.32.5 python-rich@13.7.1 python-rich-click@1.8.9 python-setuptools@80.9.0 python-simplejson@3.20.1 python-spectra@0.1.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://multiqc.info
Licenses: GPL 3+
Build system: pyproject
Synopsis: Aggregate bioinformatics analysis reports
Description:

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.

hh-suite 3.3.0
Dependencies: openmpi@4.1.6 simde@0.8.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
Licenses: GPL 3+
Build system: cmake
Synopsis: Remote protein homology detection suite
Description:

The HH-suite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

r-ewastools 1.7.2-1.f7646ca
Propagated dependencies: r-data-table@1.17.8 r-igraph@2.2.1 r-illuminaio@0.52.0 r-mblm@0.12.1 r-quadprog@1.5-8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hhhh5/ewastools/
Licenses: Unlicense
Build system: r
Synopsis: Quality control toolset for the Illumina Infinium DNA methylation
Description:

This package provides a collection of useful functions for working with DNA methylation micro-array data.

phast 1.5
Dependencies: clapack@3.2.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://compgen.cshl.edu/phast/
Licenses: Modified BSD
Build system: gnu
Synopsis: Phylogenetic analysis with space/time models
Description:

Phylogenetic Analysis with Space/Time models (PHAST) is a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.

phylip 3.697
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://evolution.genetics.washington.edu/phylip/
Licenses: FreeBSD
Build system: gnu
Synopsis: Tools for inferring phylogenies
Description:

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).

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