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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.


seqmagick 0.8.6-0.dee6ab9
Dependencies: python-biopython@1.85 python-pygtrie@2.5.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/fhcrc/seqmagick
Licenses: GPL 3
Build system: pyproject
Synopsis: Tools for converting and modifying sequence files
Description:

Bioinformaticians often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. Seqmagick is a utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

java-biojava-core 4.0.0
Propagated dependencies: java-log4j-api@2.17.1 java-log4j-core@2.17.1 java-slf4j-api@1.7.25 java-slf4j-simple@1.7.25
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biojava.org
Licenses: LGPL 2.1+
Build system: ant
Synopsis: Core libraries of Java framework for processing biological data
Description:

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

hisat2 2.2.1
Dependencies: python-wrapper@3.11.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://daehwankimlab.github.io/hisat2/
Licenses: GPL 3+
Build system: gnu
Synopsis: Graph-based alignment of genomic sequencing reads
Description:

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). In addition to using one global graph FM (GFM) index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes, combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

tetoolkit 2.2.3
Dependencies: bash-minimal@5.2.37 coreutils@9.1 bedtools@2.31.1 python-pysam@0.23.0 r-minimal@4.5.2 r-deseq2@1.50.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mhammell-laboratory/TEtranscripts
Licenses: GPL 3+
Build system: pyproject
Synopsis: Transposable elements in differential enrichment analysis
Description:

This is package for including transposable elements in differential enrichment analysis of sequencing datasets. TEtranscripts and TEcount take RNA-seq (and similar data) and annotates reads to both genes and transposable elements. TEtranscripts then performs differential analysis using DESeq2. Note that TEtranscripts and TEcount rely on specially curated GTF files, which are not included due to their size.

python-bx-python 0.14.0
Dependencies: zlib@1.3.1
Propagated dependencies: python-numpy@1.26.4 python-pyparsing@3.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/bxlab/bx-python
Licenses: Expat
Build system: pyproject
Synopsis: Tools for manipulating biological data
Description:

bx-python provides tools for manipulating biological data, particularly multiple sequence alignments.

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-skitools 0.0.0.9000-2.ba322dc
Propagated dependencies: r-biostrings@2.78.0 r-complexheatmap@2.26.0 r-data-table@1.17.8 r-devtools@2.4.6 r-dt@0.34.0 r-gchain@0.2.0-2.19f8bb9 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gplots@3.2.0 r-gutils@0.2.0-2.fc24db6 r-htmlwidgets@1.6.4 r-hwriter@1.3.2.1 r-igraph@2.2.1 r-iranges@2.44.0 r-plotly@4.11.0 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-stringr@1.6.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/skitools/
Licenses: Expat
Build system: r
Synopsis: Various mskilab R utilities
Description:

This package provides R miscellaneous utilities for basic data manipulation, debugging, visualization, lsf management, and common mskilab tasks.

python-htsget 0.2.6
Propagated dependencies: python-humanize@4.14.0 python-requests@2.32.5 python-six@1.17.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pypi.org/project/htsget/
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Python API and command line interface for the GA4GH htsget API
Description:

This package is a client implementation of the GA4GH htsget protocol. It provides a simple and reliable way to retrieve genomic data from servers supporting the protocol.

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.

blast+ 2.17.0
Dependencies: bzip2@1.0.8 lmdb@0.9.29 zlib@1.3.1 pcre@8.45 perl@5.36.0 python-wrapper@3.11.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://blast.ncbi.nlm.nih.gov
Licenses: Public Domain Expat Boost 1.0 LGPL 2.0+ ASL 2.0
Build system: gnu
Synopsis: Basic local alignment search tool
Description:

BLAST is a popular method of performing a DNA or protein sequence similarity search, using heuristics to produce results quickly. It also calculates an “expect value” that estimates how many matches would have occurred at a given score by chance, which can aid a user in judging how much confidence to have in an alignment.

r-cssam 1.4-1.9ec58c9
Propagated dependencies: r-formula@1.2-5 r-ggplot2@4.0.1 r-pkgmaker@0.32.10 r-plyr@1.8.9 r-rngtools@1.5.2 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/shenorrLab/csSAM/
Licenses: LGPL 2.1+
Build system: r
Synopsis: Cell type-specific statistical analysis of microarray
Description:

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

porechop 0.2.3-1.289d5dc
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rrwick/porechop
Licenses: GPL 3+
Build system: pyproject
Synopsis: Finding, trimming or splitting adapters, in Oxford Nanopore reads
Description:

The porechop package is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

pigx-sars-cov-2 0.0.9
Dependencies: bash-minimal@5.2.37 bedtools@2.31.1 bwa@0.7.18 ensembl-vep@112 fastp@0.23.2 fastqc@0.11.9 ivar@1.4.4 kraken2@2.1.2 krona-tools@2.8 lofreq@2.1.5 multiqc@1.14 python-pyyaml@6.0.2 python-wrapper@3.11.14 r-base64url@1.4 r-data-table@1.17.8 r-deconvr@1.16.0 r-dplyr@1.1.4 r-dt@0.34.0 r-ggplot2@4.0.1 r-htmltools@0.5.8.1 r-jsonlite@2.0.0 r-knitr@1.50 r-magrittr@2.0.4 r-mass@7.3-65 r-minimal@4.5.2 r-plotly@4.11.0 r-qpcr@1.4-2 r-r-utils@2.13.0 r-reshape2@1.4.5 r-rmarkdown@2.30 r-stringr@1.6.0 r-tidyr@1.3.1 r-viridis@0.6.5 samtools@1.19 snakemake@7.32.4 wget@1.25.0
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 wastewater sequencing
Description:

PiGx SARS-CoV-2 is a pipeline for analysing data from sequenced wastewater samples and identifying given variants-of-concern of SARS-CoV-2. The pipeline can be used for continuous sampling. The output report will provide an intuitive visual overview about the development of variant abundance over time and location.

r-readwriter 1.5.3-1.91373c4
Propagated dependencies: r-gtools@3.9.5 r-openxlsx@4.2.8.1 r-readr@2.1.6 r-stringendo@0.6.0-1.15594b1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/ReadWriter
Licenses: GPL 3
Build system: r
Synopsis: Functions to read and write files conveniently
Description:

ReadWriter is a set of R functions to read and write files conveniently.

hmmer 3.3.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://hmmer.org/
Licenses: Modified BSD
Build system: gnu
Synopsis: Biosequence analysis using profile hidden Markov models
Description:

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

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.

gdcm 3.2.2
Dependencies: charls@2.4.2 expat@2.7.1 json-c@0.18 openssl@3.0.8 util-linux@2.40.4 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/gdcm/
Licenses: Modified BSD
Build system: cmake
Synopsis: Grassroots DICOM library
Description:

Grassroots DICOM (GDCM) is an implementation of the DICOM standard designed to be open source so that researchers may access clinical data directly. GDCM includes a file format definition and a network communications protocol, both of which should be extended to provide a full set of tools for a researcher or small medical imaging vendor to interface with an existing medical database.

bioparser 3.0.13
Dependencies: biosoup@0.10.0
Propagated dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rvaser/bioparser
Licenses: Expat
Build system: cmake
Synopsis: C++ library for parsing several formats in bioinformatics
Description:

Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

rsem 1.3.3
Dependencies: bash-minimal@5.2.37 boost@1.83.0 r-minimal@4.5.2 perl@5.36.0 htslib@1.3.1 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://deweylab.biostat.wisc.edu/rsem/
Licenses: GPL 3+
Build system: gnu
Synopsis: Estimate gene expression levels from RNA-Seq data
Description:

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides a user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, it can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

r-anndatar 0.99.0-1.5c3eb7e
Propagated dependencies: r-matrix@1.7-4 r-r6@2.6.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/scverse/anndataR
Licenses: Expat
Build system: r
Synopsis: AnnData interoperability in R
Description:

This package aims to bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyze your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.

python-coolbox 0.3.8
Dependencies: pybind11@2.13.6
Propagated dependencies: python-cooler@0.9.3 python-dna-features-viewer@3.1.1 python-fire@0.7.0 python-h5py@3.13.0 python-intervaltree@3.1.0 python-ipywidgets@8.1.2 jupyter@1.0.0 python-matplotlib@3.8.2 python-nbformat@5.10.4 python-numpy@1.26.4 python-numpydoc@1.5.0 python-pandas@2.2.3 python-pybbi@0.4.1 python-pytest@8.4.1 python-scipy@1.12.0 python-statsmodels@0.14.4 python-strawc@0.0.2.1 python-svgutils@0.3.4 python-termcolor@2.5.0 python-voila@0.5.8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/GangCaoLab/CoolBox
Licenses: GPL 3+
Build system: python
Synopsis: Genomic data visualization toolkit
Description:

CoolBox is a toolkit for visual analysis of genomics data. It aims to be highly compatible with the Python ecosystem, easy to use and highly customizable with a well-designed user interface. It can be used in various visualization situations, for example, to produce high-quality genome track plots or fetch common used genomic data files with a Python script or command line, interactively explore genomic data within Jupyter environment or web browser.

python-genomepy 0.15.0
Propagated dependencies: python-appdirs@1.4.4 python-biopython@1.85 python-click@8.1.8 python-colorama@0.4.6 python-diskcache@5.6.3 python-filelock@3.16.1 python-loguru@0.7.2 python-mygene@3.2.2 python-mysql-connector-python@8.0.33 python-norns@0.1.6 python-numpy@1.26.4 python-pandas@2.2.3 python-pyfaidx@0.7.2.1 python-requests@2.32.5 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://vanheeringen-lab.github.io/genomepy/
Licenses: Expat
Build system: pyproject
Synopsis: Genes and genomes at your fingertips
Description:

genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes

  1. searching available data,

  2. showing the available metadata,

  3. automatically downloading, preprocessing and matching data, and

  4. generating optional aligner indexes.

All with sensible, yet controllable defaults.

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.

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