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Bioconductor - GenomicAlignments

GenomicAlignments

This is the released version of GenomicAlignments; for the devel version, see GenomicAlignments.

Representation and manipulation of short genomic alignments

Bioconductor version: Release (3.21)

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Author: Hervé Pagès [aut, cre], Valerie Obenchain [aut], Martin Morgan [aut], Fedor Bezrukov [ctb], Robert Castelo [ctb], Halimat C. Atanda [ctb] (Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML.)

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("GenomicAlignments")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomicAlignments")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicAlignments")
Details biocViews Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software Version 1.44.0 In Bioconductor since BioC 2.14 (R-3.1) (11 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), GenomeInfoDb(>= 1.13.1), GenomicRanges(>= 1.55.3), SummarizedExperiment(>= 1.9.13), Biostrings(>= 2.55.7), Rsamtools(>= 1.31.2) Imports methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel System Requirements URL https://bioconductor.org/packages/GenomicAlignments Bug Reports https://github.com/Bioconductor/GenomicAlignments/issues See More Suggests ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle Linking To S4Vectors, IRanges Enhances Depends On Me AllelicImbalance, Basic4Cseq, ChIPexoQual, groHMM, HelloRanges, hiReadsProcessor, igvR, ORFik, prebs, recoup, RiboDiPA, ShortRead, SplicingGraphs, sequencing Imports Me AneuFinder, APAlyzer, ASpli, ATACseqQC, ATACseqTFEA, atena, BaalChIP, bambu, biovizBase, breakpointR, CAGEfightR, CAGEr, cfDNAPro, chimeraviz, ChIPpeakAnno, ChIPQC, CNEr, consensusDE, CoverageView, CrispRVariants, crupR, CSSQ, customProDB, DAMEfinder, DegNorm, derfinder, DEScan2, DiffBind, DNAfusion, DuplexDiscovereR, easyRNASeq, esATAC, FLAMES, FRASER, gcapc, gDNAx, genomation, GenomicFiles, GenomicPlot, ggbio, gmapR, gmoviz, GreyListChIP, GUIDEseq, Gviz, icetea, IMAS, INSPEcT, IntEREst, MADSEQ, MDTS, metagene2, metaseqR2, methylPipe, mosaics, Motif2Site, MotifPeeker, msgbsR, NADfinder, PICB, PICS, plyranges, pram, proActiv, raer, ramwas, Repitools, RiboProfiling, ribosomeProfilingQC, RNAmodR, roar, Rqc, rtracklayer, saseR, scPipe, scruff, seqsetvis, SGSeq, soGGi, spiky, SPLINTER, srnadiff, strandCheckR, TAPseq, TCseq, trackViewer, transcriptR, Ularcirc, UMI4Cats, VaSP, VplotR, ZygosityPredictor, leeBamViews, alakazam, iimi, MAAPER, PACVr, VALERIE Suggests Me amplican, BindingSiteFinder, BiocParallel, csaw, DEXSeq, EpiCompare, ExperimentHub, extraChIPs, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, GenomicTuples, igvShiny, IRanges, QuasR, Rsamtools, SARC, similaRpeak, Streamer, systemPipeR, NanoporeRNASeq, parathyroidSE, RNAseqData.HNRNPC.bam.chr14, seqmagick Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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