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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-dirichletmultinomial 1.52.0
Dependencies: gsl@2.8
Propagated dependencies: r-biocgenerics@0.56.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DirichletMultinomial
Licenses: LGPL 3
Build system: r
Synopsis: Dirichlet-Multinomial mixture models for microbiome data
Description:

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.

r-annotationhub 4.0.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocbaseutils@1.12.0 r-biocfilecache@3.0.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-biocversion@3.22.0 r-curl@7.0.0 r-dplyr@1.1.4 r-httr2@1.2.1 r-rappdirs@0.3.3 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AnnotationHub
Licenses: Artistic License 2.0
Build system: r
Synopsis: Client to access AnnotationHub resources
Description:

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g. VCF, bed, wig) and other resources from standard locations (e.g. UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

r-variancepartition 1.40.0
Propagated dependencies: r-aod@1.3.3 r-biobase@2.70.0 r-biocparallel@1.44.0 r-corpcor@1.6.10 r-fancova@0.6-1 r-ggplot2@4.0.1 r-gplots@3.2.0 r-gtools@3.9.5 r-iterators@1.0.14 r-limma@3.66.0 r-lme4@1.1-37 r-lmertest@3.1-3 r-mass@7.3-65 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pbkrtest@0.5.5 r-rdpack@2.6.4 r-remacor@0.0.20 r-reshape2@1.4.5 r-rhpcblasctl@0.23-42 r-rlang@1.1.6 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/variancePartition/
Licenses: GPL 2+
Build system: r
Synopsis: Analyze variation in gene expression experiments
Description:

This is a package providing tools to quantify and interpret multiple sources of biological and technical variation in gene expression experiments. It uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. The package includes dream differential expression analysis for repeated measures.

r-lea 3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://membres-timc.imag.fr/Olivier.Francois/LEA/index.htm
Licenses: GPL 3
Build system: r
Synopsis: R package for landscape and ecological association studies
Description:

LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.

r-widgettools 1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/widgetTools/
Licenses: LGPL 3+
Build system: r
Synopsis: Tools for creating interactive tcltk widgets
Description:

This package contains tools to support the construction of tcltk widgets in R.

r-cytolib 2.22.0
Propagated dependencies: r-bh@1.87.0-1 r-rhdf5lib@1.32.0 r-rprotobuflib@2.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/cytolib/
Licenses: Artistic License 2.0
Build system: r
Synopsis: C++ infrastructure for working with gated cytometry
Description:

This package provides the core data structure and API to represent and interact with gated cytometry data.

r-mafh5-gnomad-v3-1-2-grch38 3.15.1
Propagated dependencies: r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-genomicscores@2.22.0 r-hdf5array@1.38.0 r-iranges@2.44.0 r-rhdf5@2.54.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MafH5.gnomAD.v3.1.2.GRCh38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from gnomAD version 3.1.2 for GRCh38
Description:

This package is designed to store minor allele frequency data. It retrieves this data from the Genome Aggregation Database (gnomAD version 3.1.2) for the human genome version GRCh38.

r-affxparser 1.82.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/HenrikBengtsson/affxparser
Licenses: LGPL 2.0+ LGPL 2.1 GPL 2
Build system: r
Synopsis: Affymetrix File Parsing SDK
Description:

This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

r-biocstyle 2.38.0
Propagated dependencies: r-biocmanager@1.30.27 r-bookdown@0.45 r-knitr@1.50 r-rmarkdown@2.30 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocStyle
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bioconductor formatting styles
Description:

This package provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

r-tximeta 1.28.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-biocfilecache@3.0.0 r-biostrings@2.78.0 r-ensembldb@2.34.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-jsonlite@2.0.0 r-matrix@1.7-4 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-txdbmaker@1.6.0 r-tximport@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/mikelove/tximeta
Licenses: GPL 2
Build system: r
Synopsis: Transcript quantification import with automatic metadata
Description:

This package implements transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

r-fdb-infiniummethylation-hg19 2.2.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biostrings@2.78.0 r-genomicfeatures@1.62.0 r-org-hs-eg-db@3.22.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Compiled HumanMethylation27 and HumanMethylation450 annotations
Description:

This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.

r-biomvrcns 1.50.0
Propagated dependencies: r-genomicranges@1.62.0 r-gviz@1.54.0 r-iranges@2.44.0 r-mvtnorm@1.3-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biomvRCNS
Licenses: GPL 2+
Build system: r
Synopsis: Copy number study and segmentation for multivariate biological data
Description:

In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.

r-gqtlstats 1.21.3
Propagated dependencies: r-annotationdbi@1.72.0 r-batchjobs@1.10 r-bbmisc@1.13 r-beeswarm@0.4.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-doparallel@1.0.17 r-dplyr@1.1.4 r-erma@1.24.1 r-ffbase@0.13.3 r-foreach@1.5.2 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicfiles@1.46.0 r-genomicranges@1.62.0 r-ggbeeswarm@0.7.2 r-ggplot2@4.0.1 r-gqtlbase@1.21.1 r-hardyweinberg@1.7.9 r-homo-sapiens@1.3.1 r-iranges@2.44.0 r-limma@3.66.0 r-mgcv@1.9-4 r-plotly@4.11.0 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-shiny@1.11.1 r-snpstats@1.60.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/gQTLstats
Licenses: Artistic License 2.0
Build system: r
Synopsis: Computationally efficient analysis for eQTL and allied studies
Description:

This package provides tools for the computationally efficient analysis of quantitative trait loci (QTL) data, including eQTL, mQTL, dsQTL, etc. The software in this package aims to support refinements and functional interpretation of members of a collection of association statistics on a family of feature/genome hypotheses.

r-biomformat 1.38.0
Propagated dependencies: r-jsonlite@2.0.0 r-matrix@1.7-4 r-plyr@1.8.9 r-rhdf5@2.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/joey711/biomformat/
Licenses: GPL 2
Build system: r
Synopsis: Interface package for the BIOM file format
Description:

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the Python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

r-keggrest 1.50.0
Propagated dependencies: r-biostrings@2.78.0 r-httr@1.4.7 r-png@0.1-8
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/KEGGREST
Licenses: Artistic License 2.0
Build system: r
Synopsis: Client-side REST access to KEGG
Description:

This package provides a package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST server.

r-ebimage 4.52.0
Propagated dependencies: r-abind@1.4-8 r-biocgenerics@0.56.0 r-fftwtools@0.9-11 r-htmltools@0.5.8.1 r-htmlwidgets@1.6.4 r-jpeg@0.1-11 r-locfit@1.5-9.12 r-png@0.1-8 r-rcurl@1.98-1.17 r-tiff@0.1-12
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/aoles/EBImage
Licenses: LGPL 2.1+
Build system: r
Synopsis: Image processing and analysis toolbox for R
Description:

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

r-massspecwavelet 1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MassSpecWavelet/
Licenses: LGPL 2.0+
Build system: r
Synopsis: Mass spectrum processing by wavelet-based algorithms
Description:

The MassSpecWavelet package aims to process Mass Spectrometry (MS) data mainly through the use of wavelet transforms. It supports peak detection based on Continuous Wavelet Transform (CWT).

r-genomicscores 2.22.0
Propagated dependencies: r-annotationhub@4.0.0 r-biobase@2.70.0 r-biocfilecache@3.0.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-biostrings@2.78.0 r-delayedarray@0.36.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-hdf5array@1.38.0 r-httr@1.4.7 r-iranges@2.44.0 r-rhdf5@2.54.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/rcastelo/GenomicScores/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Work with genome-wide position-specific scores
Description:

This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor.

r-homo-sapiens 1.3.1
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0 r-go-db@3.22.0 r-org-hs-eg-db@3.22.0 r-organismdbi@1.52.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Homo.sapiens/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for the Homo.sapiens object
Description:

This package contains the Homo.sapiens object to access data from several related annotation packages.

r-txdb-dmelanogaster-ucsc-dm6-ensgene 3.12.0
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-genomationdata 1.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinformatics.mdc-berlin.de/genomation/
Licenses: GPL 3+
Build system: r
Synopsis: Experimental data for use with the genomation package
Description:

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.

r-organism-dplyr 1.37.1
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationfilter@1.34.0 r-biocfilecache@3.0.0 r-dbi@1.2.3 r-dbplyr@2.5.1 r-dplyr@1.1.4 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rlang@1.1.6 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Organism.dplyr
Licenses: Artistic License 2.0
Build system: r
Synopsis: Dplyr-based access to Bioconductor annotation resources
Description:

This package provides an alternative interface to Bioconductor annotation resources, in particular the gene identifier mapping functionality of the org packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the TxDb packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

r-greylistchip 1.42.0
Propagated dependencies: r-bsgenome@1.78.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-mass@7.3-65 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GreyListChIP
Licenses: Artistic License 2.0
Build system: r
Synopsis: Greylist artefact regions based on ChIP inputs
Description:

This package identifies regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling.

r-genomicdatacommons 1.34.1
Propagated dependencies: r-dplyr@1.1.4 r-genomicranges@1.62.0 r-httr@1.4.7 r-iranges@2.44.0 r-jsonlite@2.0.0 r-rappdirs@0.3.3 r-readr@2.1.6 r-rlang@1.1.6 r-tibble@3.3.0 r-tidyr@1.3.1 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GenomicDataCommons
Licenses: Artistic License 2.0
Build system: r
Synopsis: NIH/NCI genomic data commons access
Description:

This package lets you programmatically access the NIH/NCI Genomic Data Commons RESTful service.

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Total results: 68658