Package: easyRNASeq
Version: 1.6.4
Date: 2013-10-01
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 (>=
        1.16.0), Biobase (>= 2.20.1), BiocGenerics (>= 0.6.0), biomaRt
        (>= 2.16.0), edgeR (>= 3.2.4), Biostrings (>= 2.28.0), BSgenome
        (>= 1.28.0), DESeq (>= 1.12.1), GenomicRanges (>= 1.12.5),
        IRanges (>= 1.18.4), LSD (>= 2.5), Rsamtools (>= 1.12.4),
        ShortRead (>= 1.18.0)
Suggests: BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), GenomicFeatures
        (>= 1.11.0), RnaSeqTutorial (>= 0.0.11)
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: 2013-10-02 07:26:27 UTC; biocbuild
Built: R 3.0.1; ; 2013-10-02 12:01:30 UTC; windows
