Package: GenomicAlignments
Title: Representation and manipulation of short genomic alignments
Description: 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.
biocViews: Infrastructure, DataImport, Genetics, Sequencing, RNASeq,
        SNP, Coverage, Alignment, ImmunoOncology
URL: https://bioconductor.org/packages/GenomicAlignments
Video: https://www.youtube.com/watch?v=2KqBSbkfhRo ,
        https://www.youtube.com/watch?v=3PK_jx44QTs
BugReports: https://github.com/Bioconductor/GenomicAlignments/issues
Version: 1.48.0
License: Artistic-2.0
Encoding: UTF-8
Authors@R: c(
	person("Hervé", "Pagès", role=c("aut", "cre"),
		email="hpages.on.github@gmail.com"),
	person("Valerie", "Obenchain", role="aut"),
	person("Martin", "Morgan", role="aut"),
	person("Fedor", "Bezrukov", role="ctb"),
	person("Robert", "Castelo", role="ctb"),
	person("Halimat C.", "Atanda", role="ctb",
		comment="Translated 'WorkingWithAlignedNucleotides' vignette from Sweave to RMarkdown / HTML."
	))
Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=
        0.47.6), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>=
        1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>=
        2.77.2), Rsamtools (>= 2.25.1)
Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
        GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo
        (>= 0.99.2)
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, knitr, BiocStyle
Collate: utils.R cigar-utils.R GAlignments-class.R
        GAlignmentPairs-class.R GAlignmentsList-class.R
        GappedReads-class.R OverlapEncodings-class.R
        findMateAlignment.R readGAlignments.R junctions-methods.R
        sequenceLayer.R pileLettersAt.R stackStringsFromGAlignments.R
        intra-range-methods.R coverage-methods.R setops-methods.R
        findOverlaps-methods.R coordinate-mapping-methods.R
        encodeOverlaps-methods.R findCompatibleOverlaps-methods.R
        summarizeOverlaps-methods.R findSpliceOverlaps-methods.R zzz.R
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GenomicAlignments
git_branch: RELEASE_3_23
git_last_commit: 34a743a
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: yes
Packaged: 2026-04-28 22:15:57 UTC; biocbuild
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@gmail.com>
