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.
Version: 1.10.0
Encoding: UTF-8
Author: Hervé Pagès, Valerie Obenchain, Martin Morgan
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
        SNP, Coverage, Alignment
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>=
        0.9.40), IRanges (>= 2.5.36), GenomeInfoDb (>= 1.1.20),
        GenomicRanges (>= 1.25.6), SummarizedExperiment (>= 0.3.1),
        Biostrings (>= 2.37.1), Rsamtools (>= 1.21.4)
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
License: Artistic-2.0
Collate: 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
        stackStringsFromBam.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
Video: https://www.youtube.com/watch?v=2KqBSbkfhRo ,
        https://www.youtube.com/watch?v=3PK_jx44QTs
NeedsCompilation: yes
Packaged: 2016-10-17 23:21:45 UTC; biocbuild
Built: R 3.4.1; x86_64-apple-darwin14.5.0; 2017-09-22 22:11:00 UTC; unix
