rgsepd

Package: rgsepd
Type: Package
Title: Gene Set Enrichment / Projection Displays
Version: 1.4.2
Date: 2016-04-02
Author: Karl Stamm
Maintainer: Karl Stamm <karl.stamm@gmail.com>
Description: R/GSEPD is a bioinformatics package for R to help
disambiguate transcriptome samples (a matrix of RNA-Seq counts
at RefSeq IDs) by automating differential expression (with
DESeq2), then gene set enrichment (with GOSeq), and finally a
N-dimensional projection to quantify in which ways each sample
is like either treatment group.
Depends: R (>= 3.3.0), DESeq2, goseq (>= 1.17)
Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment,
hash, AnnotationDbi
Suggests: boot, tools, RUnit, BiocGenerics, knitr, xtable
License: GPL-3
biocViews: Software, DifferentialExpression, GeneSetEnrichment, RNASeq
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-05-16 05:08:53 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rgsepd' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'rgsepd'
    finding HTML links ... done
    DisplayName                             html  
    GSEPD_ChangeConditions                  html  
    GSEPD_ChangeOutput                      html  
    GSEPD_DEGHeatmap                        html  
    GSEPD_Export_DESeq                      html  
    GSEPD_Heatmap                           html  
    GSEPD_INIT                              html  
    GSEPD_PCA_Plot                          html  
    GSEPD_PCA_Spec                          html  
    GSEPD_Process                           html  
    GSEPD_ProcessAll                        html  
    GSEPD_PullDEG                           html  
    IlluminaBodymap                         html  
    IlluminaBodymapMeta                     html  
    Name_to_RefSeq                          html  
    rgsepd-package                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
* DONE (rgsepd)
Making 'packages.html' ... done