Package: rnaSeqMap
Type: Package
Title: rnaSeq analyses using xmapcore database
Version: 2.7.12
Date: 2011-05-15
Author: Anna Lesniewska <alesniewska@cs.put.poznan.pl>; Michal
        Okoniewski <michal@fgcz.ethz.ch>
Maintainer: Michal Okoniewski <michal@fgcz.ethz.ch>
Depends: R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools
Imports: GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0)
Suggests:
Description: Provides means of analysis for RNAseq data, used together
        with genomic annotation from Ensembl. Requires a set of BAM
        files on the input or alternatively, an xmapcore database in
        MySQL as a back-end, which is also a storage for sequencing
        reads. Front-end analyses include transformations of the
        coverage function, splicing analysis, finding irreducible
        regions with the two-sliding-windows algorithm and genomic
        region visualizations.
License: GPL-2
URL:
biocViews: Annotation, Bioinformatics, ReportWriting, Transcription,
        GeneExpression, DifferentialExpression,
        HighThroughputSequencing, RNAseq, SAGE, Visualization
Collate: zzz.R utils.R plots.R NucleotideDistr.R SeqReads.R NDplots.R
        NDtransforms.R bam2sig.R parseGff3.R pipelines.R
Packaged: 2011-05-16 06:47:30 UTC; biocbuild
Built: R 2.13.0; i386-pc-mingw32; 2011-05-16 13:08:56 UTC; windows
Archs: i386, x64
