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

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-shinycell 2.0.0-1.aecbd56
Propagated dependencies: r-data-table@1.17.8 r-ggplot2@4.0.1 r-glue@1.8.0 r-gridextra@2.3 r-hdf5r@1.3.12 r-matrix@1.7-4 r-r-utils@2.13.0 r-rcolorbrewer@1.1-3 r-readr@2.1.6 r-reticulate@1.44.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/SGDDNB/ShinyCell
Licenses: GPL 3
Build system: r
Synopsis: Shiny interactive web apps for single-cell data
Description:

This package provides Shiny apps for interactive exploration of single-cell data.

seqan 1.4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Build system: trivial
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.

eddylab-squid 1.9g
Dependencies: perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://eddylab.org/software.html
Licenses: GPL 2
Build system: gnu
Synopsis: C function library for sequence analysis
Description:

SQUID is Sean Eddy's personal library of C functions and utility programs for sequence analysis.

python-phylophlan 3.0.3
Propagated dependencies: python-biopython@1.85 python-dendropy@4.5.1 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-seaborn@0.13.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biobakery/phylophlan
Licenses: Expat
Build system: pyproject
Synopsis: Phylogenetic analysis of microbial isolates and genomes from metagenomes
Description:

This package is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. This software package can assign both genomes and MAGs to SGBs. PhyloPhlAn can reconstruct strain-level phylogenies using clade- specific maximally informative phylogenetic markers, and can also scale to very large phylogenies comprising >17,000 microbial species.

mudskipper 0.1.0-1.effd3fa
Dependencies: zlib@1.3.1 xz@5.4.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/OceanGenomics/mudskipper
Licenses: Modified BSD
Build system: cargo
Synopsis: Convert genomic alignments to transcriptomic BAM/RAD files
Description:

Mudskipper is a tool for projecting genomic alignments to transcriptomic coordinates.

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.

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.

python-pegasusio 0.9.1
Propagated dependencies: python-anndata@0.12.1 python-cython@3.1.2 python-docopt@0.6.2 python-h5py@3.13.0 python-loompy@3.0.7 python-natsort@8.4.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pillow@11.1.0 python-scipy@1.12.0 python-setuptools@80.9.0 python-zarr@2.18.7
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lilab-bcb/pegasusio
Licenses: Modified BSD
Build system: pyproject
Synopsis: Read or write single-cell genomics data
Description:

Pegasusio is a Python package for reading or writing single-cell genomics data.

exonerate 2.4.0
Dependencies: glib@2.83.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
Licenses: GPL 3
Build system: gnu
Synopsis: Generic tool for biological sequence alignment
Description:

Exonerate is a generic tool for pairwise sequence comparison. It allows the alignment of sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

r-singlet 0.99.26-1.765a6c4
Propagated dependencies: r-dplyr@1.1.4 r-fgsea@1.36.0 r-ggplot2@4.0.1 r-knitr@1.50 r-limma@3.66.0 r-matrix@1.7-4 r-msigdbr@25.1.1 r-rcpp@1.1.0 r-rcppml-devel@0.5.6-2.5449a5b r-reshape2@1.4.5 r-scuttle@1.20.0 r-seurat@5.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/zdebruine/singlet
Licenses: GPL 2+
Build system: r
Synopsis: Non-negative Matrix Factorization for single-cell analysis
Description:

This is a package for fast Non-negative Matrix Factorization (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.

r-ascat 2.5.2
Propagated dependencies: r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/VanLoo-lab/ascat/
Licenses: GPL 3
Build system: r
Synopsis: Allele-Specific Copy Number Analysis of Tumors in R
Description:

This package provides the ASCAT R package that can be used to infer tumour purity, ploidy and allele-specific copy number profiles.

r-catch 1.0-1.196ddd5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/zhanyinx/CaTCH_R
Licenses: GPL 2+
Build system: r
Synopsis: Call a hierarchy of domains based on Hi-C data
Description:

This package allows building the hierarchy of domains starting from Hi-C data. Each hierarchical level is identified by a minimum value of physical insulation between neighboring domains.

r-ggsankey 0.0.99999-1.be08dd0
Propagated dependencies: r-dplyr@1.1.4 r-ggplot2@4.0.1 r-magrittr@2.0.4 r-purrr@1.2.0 r-stringr@1.6.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/davidsjoberg/ggsankey
Licenses: Expat
Build system: r
Synopsis: Sankey, Alluvial and Sankey bump plots
Description:

This package provides a package that makes it easy to implement sankey, alluvial and sankey bump plots in ggplot2.

bowtie 2.3.4.3
Dependencies: tbb@2020.3 zlib@1.3.1 python-wrapper@3.11.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Licenses: GPL 3+
Build system: gnu
Synopsis: Fast and sensitive nucleotide sequence read aligner
Description:

Bowtie 2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

skewer 0-1.978e8e4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/relipmoc/skewer
Licenses: Expat
Build system: gnu
Synopsis: Bit-masked k-difference matching
Description:

Skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

python-ngesh 1.0
Propagated dependencies: python-ete3@3.1.3 python-numpy@1.26.4 python-six@1.17.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tresoldi/ngesh
Licenses: Expat
Build system: pyproject
Synopsis: Library for phylogenetic tree simulation
Description:

Ngesh is a Python library and CLI tool for simulating phylogenetic trees and data. It is intended for benchmarking phylogenetic methods, especially in historical linguistics andstemmatology. The generation of stochastic phylogenetic trees also goes by the name simulationmethods for phylogenetic trees, synthetic data generation, or just phylogenetic tree simulation.

python-peaks2utr 1.4.1
Propagated dependencies: python-asgiref@3.8.1 python-gffutils@0.13 python-importlib-resources@6.5.2 macs@2.2.9.1 python-numpy@1.26.4 python-psutil@7.0.0 python-pybedtools@0.10.0 python-pysam@0.23.0 python-requests@2.32.5 python-tqdm@4.67.1 python-typing-extensions@4.15.0 python-zipp@3.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haessar/peaks2utr
Licenses: GPL 3+
Build system: pyproject
Synopsis: Python CLI for annotating three prime UTR
Description:

This package provides a robust, parallelized Python CLI for annotating three prime UTR.

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.

r-chromvarmotifs 0.2.0-1.38bed55
Propagated dependencies: r-tfbstools@1.48.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/GreenleafLab/chromVARmotifs
Licenses: Expat
Build system: r
Synopsis: Stores motif collections for use with motifmatchr or chromVAR
Description:

This package stores motif collections as lists of position frequency matrix (PWMatrixList) objects provided by the TFBSTools package for use in R with packages like motifmatchr or chromVAR.

python-cellbender 0.2.2
Propagated dependencies: python-anndata@0.12.1 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-pyro-ppl@1.9.1 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-sphinx@7.4.7 python-sphinx-argparse@0.5.2 python-sphinx-autodoc-typehints@1.25.3 python-sphinx-rtd-theme@3.0.2 python-sphinxcontrib-programoutput@0.17 python-tables@3.10.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://cellbender.rtfd.io/
Licenses: Modified BSD
Build system: pyproject
Synopsis: Eliminate technical artifacts from single-cell RNA-seq data
Description:

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

python-parabam 3.0.1-0.be5bd35
Propagated dependencies: python-numpy@1.26.4 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cancerit/parabam
Licenses: GPL 3
Build system: pyproject
Synopsis: Parallel BAM File Analysis
Description:

Parabam is a tool for processing sequencing files in parallel. It uses Python's native multiprocessing framework to apply a user defined rule on an input file.

libsbml 5.20.5
Propagated dependencies: libxml2@2.14.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sbml.org/Software/libSBML
Licenses: LGPL 2.1+
Build system: cmake
Synopsis: Process SBML files and data streams
Description:

LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The Systems Biology Markup Language (SBML) is an interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.

r-metadeconfoundr 0.3.0-1.90aec02
Propagated dependencies: r-bigmemory@4.6.4 r-detectseparation@0.3 r-doparallel@1.0.17 r-dosnow@1.0.20 r-foreach@1.5.2 r-futile-logger@1.4.3 r-ggplot2@4.0.1 r-lme4@1.1-37 r-lmtest@0.9-40 r-reshape2@1.4.5 r-snow@0.4-4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/TillBirkner/metadeconfoundR
Licenses: GPL 2
Build system: r
Synopsis: Check multiple covariates for potential confounding effects
Description:

This package detects naive associations between omics features and metadata in cross-sectional data-sets using non-parametric tests. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests. The generated output can be graphically summarized using the built-in plotting function.

lofreq 2.1.5
Dependencies: htslib@1.21 python-wrapper@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://csb5.github.io/lofreq/
Licenses: Expat
Build system: gnu
Synopsis: Sensitive variant calling from sequencing data
Description:

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

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