Package: easyRNASeq
Version: 1.4.2
Date: 2011-10-15
Type: Package
Title: Count summarization and normalization for RNA-Seq data.
Author: Nicolas Delhomme, Ismael Padioleau
Maintainer: Nicolas Delhomme <delhomme@embl.de>
Description: Calculates the coverage of high-throughput short-reads against
    a genome of reference and summarizes it per feature of interest (e.g. exon,
    gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq'
    or 'edgeR' package.
Depends: graphics, methods, parallel, utils, genomeIntervals (>=
        1.14.0), Biobase (>= 2.18.0), BiocGenerics (>= 0.4.0), biomaRt
        (>= 2.14.0), edgeR (>= 3.0.0), Biostrings (>= 2.26.0), BSgenome
        (>= 1.26.0), DESeq (>= 1.10.0), GenomicRanges (>= 1.10.0),
        IRanges (>= 1.16.0), Rsamtools (>= 1.10.0), ShortRead (>=
        1.16.0)
Suggests: BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), GenomicFeatures
        (>= 1.10.0), RnaSeqTutorial (>= 0.0.10)
License: Artistic-2.0
LazyLoad: yes
Enhances: edgeR, genomeIntervals, DESeq, ShortRead
biocViews: GeneExpression, RNAseq, Genetics, Preprocessing
Collate: 'AllClasses.R' 'AllGenerics.R' 'DESeq-methods.R'
        'easyRNASeq-accessors.R' 'easyRNASeq-counts.R'
        'easyRNASeq-internal-annotation.R'
        'easyRNASeq-internal-counts.R' 'easyRNASeq-internal-methods.R'
        'easyRNASeq-internal-normalize.R' 'easyRNASeq-islands.R'
        'easyRNASeq-methods.R' 'easyRNASeq-normalize.R'
        'easyRNASeq-package.R' 'edgeR-methods.R'
        'genomeIntervals-methods.R' 'GenomicRanges-methods.R'
        'IRanges-methods.R' 'print-methods.R' 'ShortRead-methods.R'
        'show-methods.R' 'easyRNASeq-annotation.R' 'parallel-methods.R'
Packaged: 2012-10-18 06:07:43 UTC; biocbuild
Built: R 2.15.1; ; 2012-10-18 10:52:09 UTC; windows
