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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 | Package: GenomicRanges
Title: Representation and manipulation of genomic intervals
Description: The ability to efficiently represent and manipulate 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. Specialized containers for representing and manipulating
short alignments against a reference genome are defined in the
GenomicAlignments package.
Version: 1.16.4
Author: P. Aboyoun, H. Pages and M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, Sequencing, Annotation
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.7), IRanges (>=
1.21.33), GenomeInfoDb (>= 0.99.17)
Imports: methods, utils, stats, BiocGenerics, IRanges, XVector
LinkingTo: IRanges, XVector (>= 0.3.4)
Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2,
Biostrings (>= 2.25.3), Rsamtools (>= 1.13.53),
GenomicAlignments, rtracklayer, KEGG.db, KEGGgraph,
GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Athaliana.BioMart.plantsmart21, seqnames.db,
org.Sc.sgd.db, VariantAnnotation, edgeR, DESeq, DEXSeq,
pasilla, pasillaBamSubset, RUnit, digest, BiocStyle
License: Artistic-2.0
Collate: utils.R phicoef.R transcript-utils.R constraint.R
makeSeqnameIds.R seqinfo.R strand-utils.R range-squeezers.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
SummarizedExperiment-class.R
SummarizedExperiment-rowData-methods.R seqlevels-utils.R
resolveHits-methods.R RangesMapping-methods.R
RangedData-methods.R intra-range-methods.R
inter-range-methods.R coverage-methods.R setops-methods.R
findOverlaps-methods.R findOverlaps-GIntervalTree-methods.R
nearest-methods.R map-methods.R tile-methods.R
test_GenomicRanges_package.R zzz.R
Packaged: 2014-08-02 02:28:26 UTC; biocbuild
Built: R 3.1.1; x86_64-pc-linux-gnu; 2014-08-12 13:55:45 UTC; unix
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