Last data update: 2014.03.03

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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 <>
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,
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: ,
NeedsCompilation: yes
Packaged: 2016-06-16 04:05:54 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Alignment, Coverage, DataImport, Genetics, Infrastructure, RNASeq, SNP, Sequencing
● 0 images, 21 functions, 0 datasets
Reverse Depends: 16