DESCRIPTION

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.
Version: 1.13.1
Date: 2016-08-22
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' 'dexss.R'
biocViews: Sequencing, RNASeq,
        GeneExpression, DifferentialExpression, CellBiology,
          Classification, QualityControl