Package: dexus
Type: Package
Title: DEXUS - Identifying Differential Expression in RNA-Seq Studies
        with Unknown Conditions or without Replicates
Description: DEXUS identifies differentially expressed genes in RNA-Seq data
    under all possible study designs such as studies without replicates,
    without sample groups, and with unknown conditions. DEXUS works also for
    known conditions, for example for RNA-Seq data with two or multiple
    conditions. RNA-Seq read count data can be provided both by the S4 class
    Count Data Set and by read count matrices. Differentially expressed
    transcripts can be visualized by heatmaps, in which unknown conditions,
    replicates, and samples groups are also indicated. This software is fast
    since the core algorithm is written in C. For very large data sets, a
    parallel version of DEXUS is provided in this package. DEXUS is a
    statistical model that is selected in a Bayesian framework by an EM
    algorithm. DEXUS does not need replicates to detect differentially expressed
    transcripts, since the replicates (or conditions) are estimated by the EM
    method for each transcript. The method provides an
    informative/non-informative value to extract differentially expressed
    transcripts at a desired significance level or power.
biocViews: HighThroughputSequencing, Sequencing, Bioinformatics,
        Mus_musculus, Homo_sapiens, Zea_Mays, Macaca_mulatta,
        Pan_troglodytes, RNASeq, GeneExpression,
        DifferentialExpression, CellBiology,
        HighTroughputSequencingData, HapMap, RNAExpressionData,
        RNAseqData, Classification, QualityControl
Version: 1.0.2
Date: 2013-03-20
Maintainer: Guenter Klambauer <klambauer@bioinf.jku.at>
Author: Guenter Klambauer
License: LGPL (>= 2.0)
Depends: R (>= 2.15), methods, BiocGenerics
Suggests: parallel, statmod, stats, DESeq, RColorBrewer
Collate: 'AllClasses.R' 'AllGenerics.R' 'binomTest.R' 'normalization.R'
        'dexus.R' 'getSizeNB.R' 'functions.R' 'plot-methods.R'
        'show-methods.R' 'methodsAccess.R'
Packaged: 2013-09-07 04:15:21 UTC; biocbuild
Built: R 3.0.1; x86_64-apple-darwin10.8.0; 2013-09-07 07:26:29 UTC; unix
