DOI: 10.18129/B9.bioc.GenomicAlignments  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GenomicAlignments.

Representation and manipulation of short genomic alignments

Bioconductor version: 3.16

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]

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

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


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PDF R Script An Introduction to the GenomicAlignments Package
PDF R Script Counting reads with summarizeOverlaps
PDF R Script Overlap encodings
PDF R Script Working with aligned nucleotides
PDF   Reference Manual
Text   NEWS
Video   Reading from a BAM file - Part 1
Video   Reading from a BAM file - Part 2


biocViews Alignment, Coverage, DataImport, Genetics, ImmunoOncology, Infrastructure, RNASeq, SNP, Sequencing, Software
Version 1.34.1
In Bioconductor since BioC 2.14 (R-3.1) (9 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(>= 1.41.5), SummarizedExperiment(>= 1.9.13), Biostrings(>= 2.55.7), Rsamtools(>= 1.31.2)
Imports methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel
LinkingTo S4Vectors, IRanges
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, BiocStyle
Depends On Me AllelicImbalance, alpineData, Basic4Cseq, BasicSTARRseq, ChIPexoQual, groHMM, HelloRanges, hiReadsProcessor, igvR, ORFik, prebs, recoup, RiboDiPA, SCATEData, sequencing, ShortRead, SplicingGraphs
Imports Me alpine, AneuFinder, APAlyzer, ASpediaFI, ASpli, ATACseqQC, ATACseqTFEA, atena, BaalChIP, bambu, biovizBase, breakpointR, BRGenomics, CAGEfightR, CAGEr, cfDNAPro, chimeraviz, ChIPpeakAnno, ChIPQC, chromstaR, CNEr, consensusDE, contiBAIT, CopywriteR, CoverageView, CrispRVariants, CSSQ, customProDB, DAMEfinder, DegNorm, derfinder, DEScan2, DiffBind, DNAfusion, easyRNASeq, esATAC, exomePeak2, FRASER, FunChIP, gcapc, genomation, GenomicFiles, ggbio, gmapR, gmoviz, GreyListChIP, GUIDEseq, Gviz, HTSeqGenie, icetea, IMAS, INSPEcT, IntEREst, leeBamViews, MACPET, MADSEQ, MDTS, metagene, metagene2, metaseqR2, methylPipe, mosaics, Motif2Site, msgbsR, NADfinder, PICS, plyranges, pram, proActiv, ramwas, Rcade, Repitools, RiboProfiling, ribosomeProfilingQC, RNAmodR, roar, Rqc, rtracklayer, SCATE, scPipe, scruff, seqsetvis, SGSeq, single, soGGi, spiky, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, TAPseq, TarSeqQC, TCseq, trackViewer, transcriptR, Ularcirc, UMI4Cats, VaSP, VplotR
Suggests Me alpineData, amplican, BindingSiteFinder, BiocParallel, csaw, EpiCompare, gage, GenomeInfoDb, GenomicDataCommons, GenomicFeatures, GenomicRanges, IRanges, NanoporeRNASeq, parathyroidSE, QuasR, RNAseqData.HNRNPC.bam.chr14, Rsamtools, similaRpeak, Streamer, systemPipeR
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