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

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-conqur 2.0-1.c7a8879
Propagated dependencies: r-ade4@1.7-23 r-ape@5.8-1 r-compositions@2.0-9 r-cqrreg@1.2.1 r-doparallel@1.0.17 r-dplyr@1.1.4 r-fastdummies@1.7.5 r-glmnet@4.1-10 r-gplots@3.2.0 r-gunifrac@1.9 r-quantreg@6.1 r-randomforest@4.7-1.2 r-rocr@1.0-11 r-vegan@2.7-2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/wdl2459/ConQuR
Licenses: GPL 3
Build system: r
Synopsis: Batch effects removal for microbiome data
Description:

This package conducts batch effects removal from a taxa read count table by a conditional quantile regression method. The distributional attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.

python-mudata 0.3.2
Propagated dependencies: python-anndata@0.12.1 python-h5py@3.13.0 python-pandas@2.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/scverse/mudata
Licenses: Modified BSD
Build system: pyproject
Synopsis: Python package for multi-omics data analysis
Description:

Mudata is a Python package for multi-omics data analysis. It is designed to provide functionality to load, process, and store multimodal omics data.

python-scdamandtools 1.0
Propagated dependencies: python-h5py@3.13.0 python-numpy@1.26.4 python-sortedcontainers@2.4.0 python-pandas@2.2.3 python-pysam@0.23.0 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/KindLab/scDamAndTools
Licenses: Expat
Build system: pyproject
Synopsis: Functions for processing raw scDam&T-seq data
Description:

This is a set of functions for processing raw scDam&T-seq data. scDam&T-seq is a method to simultaneously measure protein-DNA interactions and transcription from single cells (Rooijers et al., 2019). It combines a DamID-based method to measure protein-DNA interactions and an adaptation of CEL-Seq to measure transcription. The starting point of the workflow is raw sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq counts.

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.

go-github-com-biogo-graph 0.0.0-20150317020928-057c1989faed
Propagated dependencies: go-gopkg-in-check-v1@1.0.0-20201130134442-10cb98267c6c
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biogo/graph
Licenses: Modified BSD
Build system: go
Synopsis: Undirected graph analysis for biogo
Description:

The package graph implements graph manipulation functions.

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.

python-iced 0.5.13
Propagated dependencies: python-numpy@1.26.4 python-pandas@2.2.3 python-scipy@1.12.0 python-scikit-learn@1.7.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hiclib/iced
Licenses: Modified BSD
Build system: pyproject
Synopsis: ICE normalization
Description:

This is a package for normalizing Hi-C contact counts efficiently.

crossmap 0.6.1
Dependencies: python-bx-python@0.14.0 python-numpy@1.26.4 python-pybigwig@0.3.22 python-pysam@0.23.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://crossmap.sourceforge.net/
Licenses: GPL 2+
Build system: pyproject
Synopsis: Convert genome coordinates between assemblies
Description:

CrossMap is a program for conversion of genome coordinates or annotation files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

imp 2.23.0
Dependencies: boost@1.59.0 cereal@1.3.2 cgal@5.6.1 gsl@2.8 hdf5@1.14.6 fftw@3.3.10 eigen@3.4.0 opencv@4.12.0
Propagated dependencies: python-numpy@1.26.4 python-scipy@1.12.0 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-networkx@3.4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://integrativemodeling.org
Licenses: LGPL 2.1+ GPL 3+
Build system: cmake
Synopsis: Integrative modeling platform
Description:

IMP's broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. IMP provides a C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way.

python-bioframe 0.6.4
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-pyyaml@6.0.2 python-requests@2.32.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/open2c/bioframe
Licenses: Expat
Build system: pyproject
Synopsis: Pandas utilities for tab-delimited and other genomic files
Description:

This package is a library to enable flexible and scalable operations on genomic interval dataframes in Python. Bioframe enables access to a rich set of dataframe operations. Working in Python enables rapid visualization and iteration of genomic analyses. The philosophy underlying bioframe is to enable flexible operations. Instead of creating a function for every possible use-case, we encourage users to compose functions to achieve their goals.

r-hdwgcna 0.4.00-1.950b8c7
Propagated dependencies: r-dplyr@1.1.4 r-enrichr@3.4 r-geneoverlap@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggraph@2.2.2 r-ggrepel@0.9.6 r-harmony@1.2.4 r-igraph@2.2.1 r-matrix@1.7-4 r-proxy@0.4-27 r-seurat@5.3.1 r-tester@0.3.0 r-tidygraph@1.3.1 r-ucell@2.14.0 r-wgcna@1.73
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/smorabit/hdWGCNA
Licenses: GPL 3
Build system: r
Synopsis: Weighted gene co-expression network analysis
Description:

hdWGCNA is an R package for performing weighted gene co-expression network analysis in high dimensional -omics such as single-cell RNA-seq or spatial transcriptomics.

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.

vsearch 2.9.1
Dependencies: zlib@1.3.1 bzip2@1.0.8 cityhash@1.1-2.8af9b8c
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/torognes/vsearch
Licenses: GPL 3 FreeBSD
Build system: gnu
Synopsis: Sequence search tools for metagenomics
Description:

VSEARCH supports DNA sequence searching, clustering, chimera detection, dereplication, pairwise alignment, shuffling, subsampling, sorting and masking. The tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch).

r-tsis 0.2.0-1.2446029
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/wyguo/TSIS
Licenses: GPL 3
Build system: r
Synopsis: Time-series isoform switch of alternative splicing
Description:

TSIS is used for detecting transcript isoform switches in time-series data. Transcript isoform switches occur when a pair of alternatively spliced isoforms reverse the order of their relative expression levels. TSIS characterizes the transcript switch by defining the isoform switch time-points for any pair of transcript isoforms within a gene. In addition, this tool describes the switch using five different features or metrics. Also it filters the results with user’s specifications and visualizes the results using different plots for the user to examine further details of the switches.

r-psupertime 0.2.6-1.73825a2
Propagated dependencies: r-cowplot@1.2.0 r-data-table@1.17.8 r-fastcluster@1.3.0 r-forcats@1.0.1 r-ggplot2@4.0.1 r-glmnet@4.1-10 r-knitr@1.50 r-matrix@1.7-4 r-rcolorbrewer@1.1-3 r-scales@1.4.0 r-scran@1.38.0 r-singlecellexperiment@1.32.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-topgo@2.62.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/wmacnair/psupertime
Licenses: GPL 3
Build system: r
Synopsis: Psupertime is supervised pseudotime for single cell RNAseq data
Description:

Psupertime is supervised pseudotime for single cell RNAseq data. It uses single cell RNAseq data, where the cells have a known ordering. This ordering helps to identify a small number of genes which place cells in that known order. It can be used for discovery of relevant genes, for identification of subpopulations, and characterization of further unknown or differently labelled data.

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-biom-format 2.1.16
Propagated dependencies: python-anndata@0.12.1 python-click@8.1.8 python-flake8@7.1.1 python-future@1.0.0 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://www.biom-format.org
Licenses: Modified BSD
Build system: pyproject
Synopsis: Biological Observation Matrix (BIOM) format utilities
Description:

The BIOM file format is designed to be a general-use format for representing counts of observations e.g. operational taxonomic units, KEGG orthology groups or lipid types, in one or more biological samples e.g. microbiome samples, genomes, metagenomes.

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-signac 1.12.0-1.8ecdde2
Dependencies: zlib@1.3.1
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-fastmatch@1.1-6 r-future@1.68.0 r-future-apply@1.20.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-irlba@2.3.5.1 r-matrix@1.7-4 r-patchwork@1.3.2 r-pbapply@1.7-4 r-rcpp@1.1.0 r-rcpproll@0.3.1 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-scales@1.4.0 r-seuratobject@5.2.0 r-stringi@1.8.7 r-tidyr@1.3.1 r-tidyselect@1.2.1 r-vctrs@0.6.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/timoast/signac/
Licenses: Expat
Build system: r
Synopsis: Analysis of single-cell chromatin data
Description:

This package provides a framework for the analysis and exploration of single-cell chromatin data. The Signac package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.

hisat 0.1.6
Dependencies: perl@5.36.0 python@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ccb.jhu.edu/software/hisat/index.shtml
Licenses: GPL 3+
Build system: gnu
Synopsis: Hierarchical indexing for spliced alignment of transcripts
Description:

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome. These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.

python-mgatk 0.7.0
Propagated dependencies: python-biopython@1.85 python-click@8.1.8 python-numpy@1.26.4 python-optparse-pretty@0.1.1 python-pandas@2.2.3 python-pysam@0.23.0 python-regex@2024.11.6 python-ruamel.yaml@0.18.14 python-setuptools@80.9.0 snakemake@8.29.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/caleblareau/mgatk
Licenses: Expat
Build system: pyproject
Synopsis: Mitochondrial genome analysis toolkit
Description:

This package is a Python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. The mgatk package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

genrich 0.5
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jsh58/Genrich
Licenses: Expat
Build system: gnu
Synopsis: Detecting sites of genomic enrichment
Description:

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

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.

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Total results: 69112