GenomicAlignments : Representation and manipulation of short genomic alignments

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: 1.8.3
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 (>= 1.24.2), 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: 2016-06-16 04:05:54 UTC; biocbuild