dexus

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: 1.12.0
Date: 2015-01-27
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
NeedsCompilation: yes
Packaged: 2016-05-04 04:53:27 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'dexus' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c dexus.cpp -o dexus.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o dexus.so dexus.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/dexus/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'dexus'
** help
*** installing help indices
  converting help for package 'dexus'
    finding HTML links ... done
    DEXUSResult-class                       html  
    DEXUSResult-subset                      html  
    INI                                     html  
    INIThreshold-set                        html  
    accessors                               html  
    countsBottomly                          html  
    countsGilad                             html  
    countsLi                                html  
    countsMontgomery                        html  
    countsPickrell                          html  
    dexss                                   html  
    dexus                                   html  
    dexus.parallel                          html  
    getSizeNB                               html  
    normalizeData                           html  
    plot                                    html  
    sort                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dexus)
Making 'packages.html' ... done