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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 45 46 47 48 49 50 | Package: GenomicRanges
Title: Representation and manipulation of genomic intervals and
variables defined along a genome
Description: The ability to efficiently represent and manipulate genomic
annotations and alignments is playing a central role when it comes
to analyzing high-throughput sequencing data (a.k.a. NGS data).
The GenomicRanges package defines general purpose containers for
storing and manipulating genomic intervals and variables defined along
a genome. More specialized containers for representing and manipulating
short alignments against a reference genome, or a matrix-like
summarization of an experiment, are defined in the GenomicAlignments
and SummarizedExperiment packages respectively. Both packages build
on top of the GenomicRanges infrastructure.
Version: 1.22.0
Encoding: UTF-8
Author: P. Aboyoun, H. Pagès, and M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
GenomeAnnotation
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>=
0.7.18), IRanges (>= 2.3.24), GenomeInfoDb (>= 1.1.20)
Imports: utils, stats, XVector
LinkingTo: S4Vectors, IRanges
Suggests: Biobase, AnnotationDbi (>= 1.21.1), annotate, Biostrings (>=
2.25.3), Rsamtools (>= 1.13.53), SummarizedExperiment (>=
0.1.5), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq,
DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2,
KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db,
org.Sc.sgd.db, pasilla, pasillaBamSubset,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene
License: Artistic-2.0
Collate: utils.R phicoef.R transcript-utils.R constraint.R
strand-utils.R range-squeezers.R GenomicRanges-class.R
GRanges-class.R DelegatingGenomicRanges-class.R GNCList-class.R
GIntervalTree-class.R GenomicRanges-comparison.R
GenomicRangesList-class.R GRangesList-class.R
makeGRangesFromDataFrame.R SummarizedExperiment-class.R
SummarizedExperiment-rowData-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
mapCoords-methods.R absoluteRanges.R tileGenome.R
tile-methods.R genomicvars.R test_GenomicRanges_package.R zzz.R
NeedsCompilation: yes
Packaged: 2015-10-14 01:30:57 UTC; biocbuild
Built: R 3.2.2; x86_64-pc-linux-gnu; "Fri, 30 Oct 2015 08:55:15 +0100"; unix
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