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    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
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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.


r-screpertoire 2.4.0
Propagated dependencies: r-assertthat@0.2.1 r-cubature@2.1.3 r-dplyr@1.1.4 r-evmix@2.12 r-ggalluvial@0.12.5 r-ggdendro@0.2.0 r-ggplot2@3.5.2 r-ggraph@2.2.1 r-igraph@2.1.4 r-inext@3.0.1 r-lifecycle@1.0.4 r-plyr@1.8.9 r-purrr@1.0.4 r-quantreg@6.1 r-rcpp@1.0.14 r-reshape2@1.4.4 r-rjson@0.2.23 r-rlang@1.1.6 r-s4vectors@0.46.0 r-seuratobject@5.1.0 r-singlecellexperiment@1.30.1 r-stringdist@0.9.15 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-tidygraph@1.3.1 r-truncdist@1.0-2 r-vgam@1.1-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scRepertoire
Licenses: GPL 2
Synopsis: Toolkit for single-cell immune receptor profiling
Description:

The scRepertoire package was built to process data derived from the 10x Genomics Chromium Immune Profiling for both TCR and Ig enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages. It also allows for general analysis of single-cell clonotype information without the use of expression information. The package functions as a wrapper for Startrac and powerTCR R packages.

r-chromstar 1.32.0
Propagated dependencies: r-bamsignals@1.40.0 r-biocgenerics@0.54.0 r-chromstardata@1.34.0 r-doparallel@1.0.17 r-foreach@1.5.2 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-iranges@2.42.0 r-mvtnorm@1.3-3 r-reshape2@1.4.4 r-rsamtools@2.24.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ataudt/chromstaR
Licenses: Artistic License 2.0
Synopsis: Chromatin state analysis for ChIP-Seq data
Description:

This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.

r-rtracklayer 1.68.0
Dependencies: openssl@3.0.8 zlib@1.3.1
Propagated dependencies: r-biocgenerics@0.54.0 r-biocio@1.18.0 r-biostrings@2.76.0 r-curl@6.2.3 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-httr@1.4.7 r-iranges@2.42.0 r-restfulr@0.0.15 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-xml@3.99-0.18 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/rtracklayer
Licenses: Artistic License 2.0
Synopsis: R interface to genome browsers and their annotation tracks
Description:

rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

r-aneufinderdata 1.36.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AneuFinderData/
Licenses: Artistic License 2.0
Synopsis: Data package for @code{AneuFinder}
Description:

This package contains whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.

r-rpx 2.16.0
Propagated dependencies: r-biocfilecache@2.16.0 r-curl@6.2.3 r-jsonlite@2.0.0 r-rcurl@1.98-1.17 r-xml2@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/lgatto/rpx
Licenses: GPL 2
Synopsis: R interface to the ProteomeXchange Repository
Description:

The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.

r-anvilgcp 1.2.0
Propagated dependencies: r-anvilbase@1.2.0 r-biocbaseutils@1.10.0 r-dplyr@1.1.4 r-httr@1.4.7 r-jsonlite@2.0.0 r-rlang@1.1.6 r-tibble@3.2.1 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Bioconductor/AnVILGCP
Licenses: Artistic License 2.0
Synopsis: GCP R client for the AnVIL
Description:

The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to work with the AnVIL package. User-level interaction with this package should be minimal.

r-hellorangesdata 1.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HelloRangesData
Licenses: GPL 2+
Synopsis: Data for the HelloRanges tutorial vignette
Description:

This package provides the data that were used in the http://quinlanlab.org/tutorials/bedtools/bedtools.html. It includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R.

r-psmatch 1.12.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-igraph@2.1.4 r-iranges@2.42.0 r-matrix@1.7-3 r-mscoreutils@1.20.0 r-protgenerics@1.40.0 r-qfeatures@1.18.0 r-s4vectors@0.46.0 r-spectra@1.18.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RforMassSpectrometry/PSM
Licenses: Artistic License 2.0
Synopsis: Handling and managing peptide spectrum matches
Description:

The PSMatch package helps proteomics practitioners to load, handle and manage peptide spectrum matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

r-bsgenome-btaurus-ucsc-bostau8 1.4.2
Propagated dependencies: r-bsgenome@1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/
Licenses: Artistic License 2.0
Synopsis: Full genome sequences for Bos taurus (UCSC version bosTau8)
Description:

This package provides the full genome sequences for Bos taurus (UCSC version bosTau8).

r-grohmm 1.42.0
Propagated dependencies: r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-mass@7.3-65 r-rtracklayer@1.68.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Kraus-Lab/groHMM
Licenses: GPL 3+
Synopsis: GRO-seq analysis pipeline
Description:

This package provides a pipeline for the analysis of GRO-seq data.

r-badregionfinder 1.36.0
Propagated dependencies: r-biomart@2.64.0 r-genomicranges@1.60.0 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BadRegionFinder
Licenses: LGPL 3
Synopsis: Identifying regions with bad coverage in sequence alignment data
Description:

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

r-biotmledata 1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biotmleData
Licenses: Expat
Synopsis: Example experimental microarray data set for the "biotmle" R package
Description:

This package provides microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using SummarizedExperiemnt, for use as an example with the biotmle R package.

r-annmap 1.50.0
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-dbi@1.2.3 r-digest@0.6.37 r-genefilter@1.90.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-lattice@0.22-7 r-rmysql@0.11.1 r-rsamtools@2.24.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/cruk-mi/annmap
Licenses: GPL 2
Synopsis: Genome annotation and visualisation for Affymetrix arrays and NGS analysis
Description:

This package annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided.

r-simpleaffy 2.66.0
Propagated dependencies: r-affy@1.86.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-gcrma@2.80.0 r-genefilter@1.90.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/simpleaffy/
Licenses: GPL 2+
Synopsis: Very simple high level analysis of Affymetrix data
Description:

This package provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

r-preprocesscore 1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/bmbolstad/preprocessCore
Licenses: LGPL 2.0+
Synopsis: Collection of pre-processing functions
Description:

This package provides a library of core pre-processing and normalization routines.

r-complexheatmap 2.24.0
Propagated dependencies: r-circlize@0.4.16 r-clue@0.3-66 r-codetools@0.2-20 r-colorspace@2.1-1 r-digest@0.6.37 r-doparallel@1.0.17 r-foreach@1.5.2 r-getoptlong@1.0.5 r-globaloptions@0.1.2 r-iranges@2.42.0 r-matrixstats@1.5.0 r-png@0.1-8 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jokergoo/ComplexHeatmap
Licenses: GPL 2+
Synopsis: Making Complex Heatmaps
Description:

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. This package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

r-flowviz 1.72.0
Propagated dependencies: r-biobase@2.68.0 r-flowcore@2.20.0 r-hexbin@1.28.5 r-idpmisc@1.1.21 r-kernsmooth@2.23-26 r-lattice@0.22-7 r-latticeextra@0.6-30 r-mass@7.3-65 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowViz/
Licenses: Artistic License 2.0
Synopsis: Visualization for flow cytometry
Description:

This package provides visualization tools for flow cytometry data.

r-wiggleplotr 1.32.0
Propagated dependencies: r-assertthat@0.2.1 r-cowplot@1.1.3 r-dplyr@1.1.4 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-iranges@2.42.0 r-purrr@1.0.4 r-rtracklayer@1.68.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/wiggleplotr/
Licenses: ASL 2.0
Synopsis: Make read coverage plots from BigWig files
Description:

This package provides tools to visualize read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualization of exonic read coverage.

r-chemminer 3.60.0
Propagated dependencies: r-base64enc@0.1-3 r-bh@1.87.0-1 r-biocgenerics@0.54.0 r-dbi@1.2.3 r-digest@0.6.37 r-dt@0.33 r-ggplot2@3.5.2 r-gridextra@2.3 r-jsonlite@2.0.0 r-png@0.1-8 r-rcpp@1.0.14 r-rcurl@1.98-1.17 r-rjson@0.2.23 r-rsvg@2.6.2 r-stringi@1.8.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/girke-lab/ChemmineR
Licenses: Artistic License 2.0
Synopsis: Cheminformatics toolkit for R
Description:

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. It contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

r-glimma 2.18.0
Propagated dependencies: r-deseq2@1.48.1 r-edger@4.6.2 r-htmlwidgets@1.6.4 r-jsonlite@2.0.0 r-limma@3.64.1 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Shians/Glimma
Licenses: LGPL 3
Synopsis: Interactive HTML graphics
Description:

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

r-systempiperdata 2.12.2
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-jsonlite@2.0.0 r-remotes@2.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/tgirke/systemPipeRdata
Licenses: Artistic License 2.0
Synopsis: Workflow templates and sample data
Description:

systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs.

r-pd-mapping50k-hind240 3.12.0
Propagated dependencies: r-biostrings@2.76.0 r-dbi@1.2.3 r-iranges@2.42.0 r-oligo@1.72.0 r-oligoclasses@1.70.0 r-rsqlite@2.3.11 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/pd.mapping50k.hind240
Licenses: Artistic License 2.0
Synopsis: Platform Design Info for Affymetrix Mapping50K_Hind240
Description:

This package provides platform design info for Affymetrix Mapping50K_Hind240.

r-msa 1.40.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-iranges@2.42.0 r-rcpp@1.0.14 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.bioinf.jku.at/software/msa/
Licenses: GPL 2+
Synopsis: Multiple sequence alignment
Description:

The msa package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

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Total results: 45109