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

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.


cgp-cavemanwrapper 1.16.0
Propagated dependencies: perl-file-path@2.16 perl-file-which@1.23 perl-const-fast@0.014 perl-capture-tiny@0.48 perl-ipc-system-simple@1.26 perl-try-tiny@0.31 perl-carp@1.50 perl-forks@0.36 pcap-core@3.5.0 perl@5.36.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/cancerit/cgpCaVEManWrapper
Licenses: AGPL 3+
Build system: gnu
Synopsis: Reference implementation of CGP workflow for CaVEMan
Description:

This package provides the reference implementation of CGP workflow for CaVEMan SNV analysis.

r-scriabin 0.0.0.9000-1.313d15e
Propagated dependencies: r-ade4@1.7-23 r-cellid@1.18.0 r-circlize@0.4.16 r-clipr@0.8.0 r-complexheatmap@2.26.0 r-complexheatmap@2.26.0 r-cowplot@1.2.0 r-dplyr@1.1.4 r-factoextra@1.0.7 r-fsa@0.10.0 r-genefilter@1.92.0 r-ggalluvial@0.12.5 r-ggfittext@0.10.2 r-ggplot2@4.0.1 r-ggsci@4.1.0 r-limma@3.66.0 r-magrittr@2.0.4 r-matrix@1.7-4 r-matrixstats@1.5.0 r-networkd3@0.4.1 r-nichenetr@2.0.4 r-pbapply@1.7-4 r-qlcmatrix@0.9.9 r-scales@1.4.0 r-scater@1.38.0 r-seurat@5.3.1 r-tibble@3.3.0 r-tidyft@0.9.20 r-wgcna@1.73
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/BlishLab/scriabin
Licenses: Expat
Build system: r
Synopsis: Single-cell resolved interaction analysis through binning
Description:

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.

python-pydeseq2 0.5.4
Propagated dependencies: python-anndata@0.11.4 python-formulaic@1.0.1 python-formulaic-contrasts@1.0.0 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/owkin/PyDESeq2
Licenses: Expat
Build system: pyproject
Synopsis: Python implementation of DESeq2
Description:

This package provides a python implementation of DESeq2.

python-anvio 8
Propagated dependencies: python-bottle@0.13.4 python-colored@2.3.0 python-django@5.2.8 python-ete3@3.1.3 python-illumina-utils@2.13 python-matplotlib@3.8.2 python-mistune@3.1.3 python-multiprocess@0.70.18 python-networkx@3.4.2 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-paste@3.10.1 python-plotext@5.2.8 python-psutil@7.0.0 python-pyani@0.2.12 python-pysam@0.23.0 python-requests@2.32.5 python-rich-argparse@1.7.1 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-six@1.17.0 python-statsmodels@0.14.4 python-tabulate@0.9.0 snakemake@8.29.2
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://anvio.org
Licenses: GPL 3+
Build system: pyproject
Synopsis: Analysis and visualization platform for 'omics data
Description:

Anvi’o is a comprehensive platform that brings together many aspects of today’s computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

perl-ppi-html 1.08
Dependencies: perl-css-tiny@1.20 perl-params-util@1.102 perl-ppi@1.277
Propagated dependencies: perl-module-install@1.19
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/PPI-HTML
Licenses: GPL 1+
Build system: perl
Synopsis: Generate syntax-hightlighted HTML for Perl using PPI
Description:
fastq-tools 0.8.3
Dependencies: pcre@8.45 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://homes.cs.washington.edu/~dcjones/fastq-tools/
Licenses: Expat
Build system: gnu
Synopsis: Tools to work with FASTQ files
Description:

This packages provides a collection of small and efficient programs for performing some common and uncommon tasks with FASTQ files.

seqan 3.0.2
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Build system: cmake
Synopsis: Library for nucleotide sequence analysis
Description:

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

allelecount 4.2.1
Dependencies: zlib@1.3.1 htslib@1.21 perl-pod-coverage@0.23 perl-file-which@1.23 perl-test-fatal@0.016 perl-try-tiny@0.31 samtools@1.19
Propagated dependencies: perl-const-fast@0.014 perl-sub-exporter-progressive@0.001013 perl-bio-db-hts@3.01 bioperl-minimal@1.7.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/cancerit/alleleCount
Licenses: AGPL 3+
Build system: gnu
Synopsis: Support code for NGS copy number algorithms
Description:

This package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenburg.

python-nanoget 1.19.4
Propagated dependencies: python-biopython@1.85 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/wdecoster/nanoget
Licenses: GPL 3
Build system: pyproject
Synopsis: Functions for Oxford Nanopore sequencing data and alignments
Description:

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.

freec 11.6b
Dependencies: perl@5.36.0
Propagated dependencies: r-rtracklayer@1.70.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://bioinfo-out.curie.fr/projects/freec/
Licenses: GPL 2+
Build system: gnu
Synopsis: Tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data
Description:

Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM).

star-fusion 1.0.0
Dependencies: perl@5.36.0 samtools@1.19 coreutils@9.1 gzip@1.14
Propagated dependencies: perl-carp@1.50 perl-pathtools@3.75 perl-db-file@1.858 perl-uri@5.05 perl-set-intervaltree@0.10
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/STAR-Fusion/STAR-Fusion/
Licenses: Modified BSD
Build system: gnu
Synopsis: Fusion detection based on STAR
Description:

This package provides a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). It uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. It further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

spades 4.2.0
Dependencies: bzip2@1.0.8 perl@5.36.0 python@3.11.14 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://ablab.github.io/spades/
Licenses: GPL 2
Build system: cmake
Synopsis: Genome assembly toolkit
Description:

SPAdes is an assembly toolkit containing various assembly pipelines.

pcap-core 3.5.0
Propagated dependencies: bwa@0.7.18 samtools@1.19 biobambam@0.0.191
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/ICGC-TCGA-PanCancer/PCAP-core
Licenses: GPL 2+
Build system: gnu
Synopsis: NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project
Description:
gnomad-sv-sites 2.1
Dependencies: gzip@1.14
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://gnomad.broadinstitute.org
Licenses: CC0
Build system: trivial
Synopsis: gnomAD structural variant sites
Description:

This package provides in uncompressed version of the gnomAD structural variant sites.

perl-cgpvcf 2.0.4
Propagated dependencies: perl-bio-pipeline-comparison@1.123050 perl-const-fast@0.014 perl-data-uuid@1.226 perl-datetime@1.54
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://cancerit.github.io/cgpVcf/
Licenses: AGPL 3+
Build system: gnu
Synopsis: Set of common Perl utilities for generating VCF headers
Description:

This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.

fastqc 0.11.9
Propagated dependencies: perl@5.36.0 icedtea@2.6.13
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Licenses: GPL 3+ ASL 2.0
Build system: gnu
Synopsis: A quality control tool for high throughput sequence data
Description:

FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.

spoa 4.1.5
Dependencies: bioparser@3.1.0 biosoup@0.11.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/rvaser/spoa
Licenses: Expat
Build system: cmake
Synopsis: C++ implementation of partial order alignment
Description:

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm, which is used to generate consensus sequences. It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine).

caveman 1.15.5
Dependencies: curl@8.6.0 htslib@1.21 linasm@1.13 perl@5.36.0 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://cancerit.github.io/CaVEMan/
Licenses: AGPL 3+
Build system: gnu
Synopsis: Implementation of an SNV expectation maximisation algorithm for calling single base substitutions in paired data
Description:

This package provides an implementation of the CaVEMan program. It uses an expectation maximisation approach to calling single base substitutions in paired data. It is designed for use with a compute cluster. Most steps in the program make use of an index parameter. The split step is designed to divide the genome into chunks of adjustable size to optimise for runtime/memory usage requirements.

r-rblast 0.99.4-1.2319817
Dependencies: blast+@2.17.0
Propagated dependencies: r-biostrings@2.78.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/mhahsler/rBLAST
Licenses: GPL 3
Build system: r
Synopsis: R Interface for the Basic Local Alignment Search Tool
Description:

This package provides an interface for the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This includes interfaces to blastn, blastp, blastx, and makeblastdb.

perl-findbin-libs 2.15
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/FindBin-libs
Licenses: GPL 1+
Build system: perl
Synopsis:
Description:
python-carputils 18.1-0.0b56f65
Propagated dependencies: python-numpy@1.26.4 python-ruamel.yaml@0.18.14 python-common@0.1.2 python-pydoe3@1.6.2 python-tables@3.10.2 python-scipy@1.12.0 python-matplotlib@3.8.2 python-pandas@2.2.3 python-six@1.17.0 python-dateutil@2.9.0
Channel: guix-science
Location: guix-science/packages/carputils.scm (guix-science packages carputils)
Home page: https://opencarp.org/about/opencarp-ecosystem#the-carputils-framework
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Python framework for access to openCARP
Description:

The carputils framework will be the optimal way to access openCARP for most users. This Python framework was developed to provide the means to easily encode in silico experiments including pre- and postprocessing. carputils will call the openCARP simulator.

python-common 0.1.2
Channel: guix-science
Location: guix-science/packages/carputils.scm (guix-science packages carputils)
Home page: https://pypi.org/project/common
Licenses: Expat
Build system: pyproject
Synopsis: Common tools and data structures implemented in pure Python
Description:

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

python-pydoe3 1.6.2
Propagated dependencies: python-numpy@1.26.4 python-scipy@1.12.0
Channel: guix-science
Location: guix-science/packages/carputils.scm (guix-science packages carputils)
Home page: https://github.com/relf/pyDOE3
Licenses: Modified BSD
Build system: pyproject
Synopsis: Design of experiments for Python
Description:

This package is designed to help the scientist, engineer, statistician, etc., to construct appropriate experimental designs.

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Total results: 68655