git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@87035 bc3139a8-67e5-0310-9ffc-ced21a209358
Sonali Arora authored on 04/03/2014 22:12:21
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@@ -2,47 +2,29 @@ Package: gmapR |
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Maintainer: Michael Lawrence <lawrence.michael@gene.com> |
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License: Artistic-2.0 |
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Title: Provides convenience methods to work with GMAP and GSNAP from |
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- within R |
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+ within R |
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Type: Package |
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Author: Cory Barr, Thomas Wu, Michael Lawrence |
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Description: GSNAP and GMAP are a pair of tools to align short-read |
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- data written by Tom Wu. This package provides convenience methods |
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- to work with GMAP and GSNAP from within R. In addition, it provides |
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- methods to tally alignment results on a per-nucleotide basis using |
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- the bam_tally tool. |
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-Version: 1.5.10 |
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+ data written by Tom Wu. This package provides convenience |
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+ methods to work with GMAP and GSNAP from within R. In addition, |
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+ it provides methods to tally alignment results on a |
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+ per-nucleotide basis using the bam_tally tool. |
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+Version: 1.5.11 |
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Depends: R (>= 2.15.0), methods, GenomicRanges |
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Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), |
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- GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools, |
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- Biobase, BSgenome |
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+ GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), |
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+ tools, Biobase, BSgenome |
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Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, |
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- BSgenome.Scerevisiae.UCSC.sacCer3, |
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- org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, |
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- BSgenome.Hsapiens.UCSC.hg19, LungCancerLines |
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-License: Artistic-2.0 |
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-Collate: GmapBamReader-class.R |
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- GmapGenomeDirectory-class.R |
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- GmapGenome-class.R |
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- GmapSnpDirectory-class.R |
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- GmapSnps-class.R |
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- GsnapParam-class.R |
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- GsnapOutput-class.R |
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- atoiindex-command.R |
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- BamTallyParam-class.R |
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- bam_tally-command.R |
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- cmetindex-command.R |
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- get-genome-command.R |
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- gmap-command.R |
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- gmap_build-command.R |
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- gsnap-command.R |
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- iit-format.R |
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- iit_store-command.R |
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- info.R |
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- snpindex-command.R |
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- system.R |
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- test_gmapR_package.R |
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- makeGmapGenomePackage.R |
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- TP53Genome.R |
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- utils.R |
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- asSystemCall.R |
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- |
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+ BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, |
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+ TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, |
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+ LungCancerLines |
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+Collate: GmapBamReader-class.R GmapGenomeDirectory-class.R |
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+ GmapGenome-class.R GmapSnpDirectory-class.R GmapSnps-class.R |
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+ GsnapParam-class.R GsnapOutput-class.R atoiindex-command.R |
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+ BamTallyParam-class.R bam_tally-command.R cmetindex-command.R |
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+ get-genome-command.R gmap-command.R gmap_build-command.R |
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+ gsnap-command.R iit-format.R iit_store-command.R info.R |
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+ snpindex-command.R system.R test_gmapR_package.R |
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+ makeGmapGenomePackage.R TP53Genome.R utils.R asSystemCall.R |
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+biocViews: Alignment |