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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.

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r-residualmatrix 1.20.0
Propagated dependencies: r-delayedarray@0.36.0 r-matrix@1.7-4 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/ResidualMatrix
Licenses: GPL 3
Build system: r
Synopsis: Create a DelayedMatrix of regression residuals
Description:

This package implements tools for delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. It also supports partial computation of residuals where selected factors are to be preserved in the output matrix. It implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.

r-hgu95av2-db 3.13.0
Propagated dependencies: r-annotationdbi@1.72.0 r-org-hs-eg-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hgu95av2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)
Description:

This package provides Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories.

r-breakpointrdata 1.28.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/daewoooo/breakpointRdata
Licenses: Expat
Build system: r
Synopsis: Strand-seq data for demonstration purposes
Description:

This package is a collection of Strand-seq data. The main purpose is to demonstrate functionalities of the breakpointR package.

r-csaw 1.44.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-edger@4.8.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-limma@3.66.0 r-matrix@1.7-4 r-metapod@1.18.0 r-rcpp@1.1.0 r-rhtslib@3.6.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0 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/csaw
Licenses: GPL 3
Build system: r
Synopsis: ChIP-Seq analysis with windows
Description:

This is a package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

r-webbioc 1.82.0
Dependencies: netpbm@10.78.3 perl@5.36.0
Propagated dependencies: r-affy@1.88.0 r-annaffy@1.82.0 r-biobase@2.70.0 r-biocmanager@1.30.27 r-gcrma@2.82.0 r-multtest@2.66.0 r-qvalue@2.42.0 r-vsn@3.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/
Licenses: GPL 2+
Build system: r
Synopsis: Bioconductor web interface
Description:

This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.

r-illuminahumanmethylationepicanno-ilm10b4-hg19 0.6.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://doi.org/doi:10.18129/B9.bioc.IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Illumina's EPIC methylation arrays
Description:

This is an annotation package for Illumina's EPIC methylation arrays.

r-plyranges 1.30.1
Propagated dependencies: r-biocgenerics@0.56.0 r-dplyr@1.1.4 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-magrittr@2.0.4 r-rlang@1.1.6 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-tidyselect@1.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/plyranges
Licenses: Artistic License 2.0
Build system: r
Synopsis: Fluent interface for manipulating GenomicRanges
Description:

This package provides a dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessibility for new Bioconductor users is hopefully increased.

r-beadarray 2.58.0
Propagated dependencies: r-annotationdbi@1.72.0 r-beaddatapackr@1.62.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-hexbin@1.28.5 r-illuminaio@0.52.0 r-iranges@2.44.0 r-limma@3.66.0 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/beadarray
Licenses: Expat
Build system: r
Synopsis: Quality assessment and low-level analysis for Illumina BeadArray data
Description:

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

r-maser 1.28.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-dt@0.34.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gviz@1.54.0 r-iranges@2.44.0 r-reshape2@1.4.5 r-rtracklayer@1.70.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/DiogoVeiga/maser
Licenses: Expat
Build system: r
Synopsis: Mapping alternative splicing events to proteins
Description:

This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.

r-missmethyl 1.44.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biasedurn@2.0.12 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-go-db@3.22.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-illuminahumanmethylation450kmanifest@0.4.0 r-illuminahumanmethylationepicanno-ilm10b4-hg19@0.6.0 r-illuminahumanmethylationepicmanifest@0.3.0 r-illuminahumanmethylationepicv2anno-20a1-hg38@1.0.0 r-illuminahumanmethylationepicv2manifest@1.0.0 r-iranges@2.44.0 r-limma@3.66.0 r-methylumi@2.56.0 r-minfi@1.56.0 r-org-hs-eg-db@3.22.0 r-ruv@0.9.7.1 r-s4vectors@0.48.0 r-statmod@1.5.1 r-stringr@1.6.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/missMethyl
Licenses: GPL 2
Build system: r
Synopsis: Analyzing Illumina HumanMethylation BeadChip data
Description:

This is a package for normalization, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalization procedure is subset-quantile within-array normalization (SWAN), which allows Infinium I and II type probes on a single array to be normalized together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.

r-bgeecall 1.26.0
Propagated dependencies: kallisto@0.50.1 r-annotationdbi@1.72.0 r-biostrings@2.78.0 r-curl@7.0.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomicfeatures@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-jsonlite@2.0.0 r-rcurl@1.98-1.17 r-readr@2.1.6 r-rhdf5@2.54.0 r-rslurm@0.6.2 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-scales@1.4.0 r-sjmisc@2.8.11 r-sjmisc@2.8.11 r-spatstat-univar@3.1-5 r-stringr@1.6.0 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/BgeeDB/BgeeCall
Licenses: GPL 3
Build system: r
Synopsis: RNA-Seq present/absent gene expression calls generation
Description:

BgeeCall allows generating present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee.

r-motifbreakr 2.24.0
Propagated dependencies: r-biocfilecache@3.0.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biomart@2.66.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsicons@0.1.2 r-bslib@0.9.0 r-dt@0.34.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gviz@1.54.0 r-iranges@2.44.0 r-matrixstats@1.5.0 r-motifdb@1.52.0 r-motifstack@1.54.0 r-pwalign@1.6.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-shiny@1.11.1 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tfmpvalue@0.0.9 r-variantannotation@1.56.0 r-vroom@1.6.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/motifbreakR/
Licenses: GPL 2+
Build system: r
Synopsis: Predicting disruptiveness of single nucleotide polymorphisms
Description:

This package allows biologists to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. This package gives a choice of algorithms for interrogation of genomes with motifs from public sources:

  1. a weighted-sum probability matrix;

  2. log-probabilities;

  3. weighted by relative entropy.

This package can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.

r-cner 1.46.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-annotate@1.88.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-dbi@1.2.3 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-go-db@3.22.0 r-iranges@2.44.0 r-keggrest@1.50.0 r-powerlaw@1.0.0 r-pwalign@1.6.0 r-r-utils@2.13.0 r-readr@2.1.6 r-reshape2@1.4.5 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ge11232002/CNEr
Licenses: GPL 2 non-copyleft
Build system: r
Synopsis: CNE Detection and Visualization
Description:

This package provides tools for large-scale identification and advanced visualization of sets of conserved noncoding elements.

r-msigdb 1.18.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-experimenthub@3.0.0 r-gseabase@1.72.0 r-org-hs-eg-db@3.22.0 r-org-mm-eg-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://doi.org/doi:10.18129/B9.bioc.msigdb
Licenses: CC-BY 4.0
Build system: r
Synopsis: ExperimentHub package for the molecular signatures database
Description:

R-msigdb provides the Molecular Signatures Database in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object.

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-omnipathr 3.14.0
Propagated dependencies: r-checkmate@2.3.3 r-crayon@1.5.3 r-curl@7.0.0 r-digest@0.6.39 r-dplyr@1.1.4 r-httr@1.4.7 r-igraph@2.2.1 r-jsonlite@2.0.0 r-later@1.4.4 r-logger@0.4.1 r-lubridate@1.9.4 r-magrittr@2.0.4 r-progress@1.2.3 r-purrr@1.2.0 r-r-utils@2.13.0 r-rappdirs@0.3.3 r-readr@2.1.6 r-readxl@1.4.5 r-rlang@1.1.6 r-rmarkdown@2.30 r-rsqlite@2.4.4 r-rvest@1.0.5 r-stringi@1.8.7 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-tidyselect@1.2.1 r-vctrs@0.6.5 r-withr@3.0.2 r-xml@3.99-0.20 r-xml2@1.5.0 r-yaml@2.3.10 r-zip@2.3.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://saezlab.github.io/OmnipathR/
Licenses: Expat
Build system: r
Synopsis: OmniPath web service client and more
Description:

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.

r-mosdef 1.6.0
Propagated dependencies: r-annotationdbi@1.72.0 r-clusterprofiler@4.18.2 r-deseq2@1.50.2 r-dt@0.34.0 r-ggforce@0.5.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-go-db@3.22.0 r-goseq@1.62.0 r-htmltools@0.5.8.1 r-rcolorbrewer@1.1-3 r-rlang@1.1.6 r-s4vectors@0.48.0 r-scales@1.4.0 r-summarizedexperiment@1.40.0 r-topgo@2.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/imbeimainz/mosdef
Licenses: Expat
Build system: r
Synopsis: Frequently used and useful differential expression functions
Description:

This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

r-mutationalpatterns 3.19.1
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-cowplot@1.2.0 r-dplyr@1.1.4 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggalluvial@0.12.5 r-ggdendro@0.2.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-magrittr@2.0.4 r-nmf@0.28 r-pracma@2.4.6 r-purrr@1.2.0 r-rcolorbrewer@1.1-3 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-variantannotation@1.56.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 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/MutationalPatterns/
Licenses: Expat
Build system: r
Synopsis: Extract and visualize mutational patterns in genomic data
Description:

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.

r-bsgenome-btaurus-ucsc-bostau8 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
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
Build system: r
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-milor 2.6.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocneighbors@2.4.0 r-biocparallel@1.44.0 r-biocsingular@1.26.1 r-cowplot@1.2.0 r-dplyr@1.1.4 r-edger@4.8.0 r-ggbeeswarm@0.7.2 r-ggplot2@4.0.1 r-ggraph@2.2.2 r-ggrepel@0.9.6 r-gtools@3.9.5 r-igraph@2.2.1 r-irlba@2.3.5.1 r-limma@3.66.0 r-matrix@1.7-4 r-matrixgenerics@1.22.0 r-matrixstats@1.5.0 r-numderiv@2016.8-1.1 r-patchwork@1.3.2 r-pracma@2.4.6 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rcppeigen@0.3.4.0.2 r-rcppml@0.3.7 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://marionilab.github.io/miloR
Licenses: GPL 3
Build system: r
Synopsis: Differential neighbourhood abundance testing on a graph
Description:

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model.

r-arrayquality 1.88.0
Propagated dependencies: r-gridbase@0.4-7 r-hexbin@1.28.5 r-limma@3.66.0 r-marray@1.88.0 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://arrays.ucsf.edu/
Licenses: LGPL 2.0+
Build system: r
Synopsis: Assessing array quality on spotted arrays
Description:

This package provides functions for performing print-run and array level quality assessment.

r-snpstats 1.60.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-biocgenerics@0.56.0 r-matrix@1.7-4 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/snpStats
Licenses: GPL 3
Build system: r
Synopsis: Methods for SNP association studies
Description:

This package provides classes and statistical methods for large single-nucleotide polymorphism (SNP) association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

r-enmix 1.46.0
Propagated dependencies: r-annotationhub@4.0.0 r-biobase@2.70.0 r-doparallel@1.0.17 r-dynamictreecut@1.63-1 r-experimenthub@3.0.0 r-foreach@1.5.2 r-genefilter@1.92.0 r-geneplotter@1.88.0 r-gplots@3.2.0 r-gtools@3.9.5 r-illuminaio@0.52.0 r-impute@1.84.0 r-iranges@2.44.0 r-irlba@2.3.5.1 r-matrixstats@1.5.0 r-minfi@1.56.0 r-quadprog@1.5-8 r-rpmm@1.25 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/bioc/html/ENmix.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Quality control and analysis tools for Illumina DNA methylation BeadChip
Description:

This package provides tools for quality control, analysis and visualization of Illumina DNA methylation array data.

r-ensdb-hsapiens-v75 2.99.0
Propagated dependencies: r-ensembldb@2.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EnsDb.Hsapiens.v75
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ensembl based annotation package
Description:

This package exposes an annotation database generated from Ensembl.

Page: 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Total results: 69112