/usr/lib/R/site-library/GenomicAlignments/DESCRIPTION is in r-bioc-genomicalignments 1.14.1-1.
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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 | 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: 1.14.1
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 (>=
0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.13.1),
GenomicRanges (>= 1.29.14), SummarizedExperiment (>= 1.5.3),
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: utils.R 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: 2017-11-18 00:39:08 UTC; biocbuild
Built: R 3.4.3; x86_64-pc-linux-gnu; 'Wed, 28 Feb 2018 23:49:37 +0100'; unix
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