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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | Package: GenomicRanges
Title: Representation and manipulation of genomic intervals
Description: The ability to efficiently store genomic annotations and
alignments is playing a central role when it comes to analyze
high-throughput sequencing data (a.k.a. NGS data). The package
defines general purpose containers for storing genomic intervals
as well as more specialized containers for storing alignments
against a reference genome.
Version: 1.14.3
Author: P. Aboyoun, H. Pages and M. Lawrence
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
biocViews: Genetics, Sequencing, HighThroughputSequencing, Annotation
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.7), IRanges (>=
1.20.3), XVector (>= 0.1.3)
Imports: methods, utils, stats, BiocGenerics, IRanges
LinkingTo: IRanges, XVector
Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Dmelanogaster.UCSC.dm3, Biostrings (>= 2.25.3),
Rsamtools (>= 1.13.53), rtracklayer, KEGG.db, KEGGgraph,
GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene, seqnames.db, org.Sc.sgd.db,
VariantAnnotation, edgeR, DESeq, DEXSeq, pasilla,
pasillaBamSubset, RUnit, digest, BiocStyle
License: Artistic-2.0
Collate: utils.R phicoef.R cigar-utils.R transcript-utils.R
constraint.R makeSeqnameIds.R seqinfo.R strand-utils.R
Seqinfo-class.R GenomicRanges-class.R GRanges-class.R
GIntervalTree-class.R GenomicRanges-comparison.R
GenomicRangesList-class.R GRangesList-class.R
makeGRangesFromDataFrame.R tileGenome.R GAlignments-class.R
GAlignmentPairs-class.R GAlignmentsList-class.R
SummarizedExperiment-class.R
SummarizedExperiment-rowData-methods.R seqlevels-utils.R
resolveHits-methods.R summarizeOverlaps.R
RangesMapping-methods.R RangedData-methods.R
intra-range-methods.R inter-range-methods.R setops-methods.R
findOverlaps-methods.R findOverlaps-GIntervalTree-methods.R
nearest-methods.R encodeOverlaps-methods.R coverage-methods.R
findSpliceOverlaps-methods.R findSpliceOverlaps-utils.R
test_GenomicRanges_package.R zzz.R
Packaged: 2013-10-29 04:05:42 UTC; biocbuild
Built: R 3.0.2; x86_64-pc-linux-gnu; 2013-11-27 11:09:32 UTC; unix
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