DEXSeq

Package: DEXSeq
Version: 1.18.4
Title: Inference of differential exon usage in RNA-Seq
Author: Simon Anders <sanders@fs.tum.de> and Alejandro Reyes
<alejandro.reyes@embl.de>
Maintainer: Alejandro Reyes <alejandro.reyes@embl.de>
Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>=
2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11),
AnnotationDbi, RColorBrewer, S4Vectors
Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22),
parathyroidSE, BiocStyle, knitr
Enhances:
Description: The package is focused on finding differential exon usage
using RNA-seq exon counts between samples with different
experimental designs. It provides functions that allows the
user to make the necessary statistical tests based on a model
that uses the negative binomial distribution to estimate the
variance between biological replicates and generalized linear
models for testing. The package also provides functions for the
visualization and exploration of the results.
License: GPL (>= 3)
URL:
biocViews: Sequencing, RNASeq, DifferentialExpression
Packaged: 2016-05-19 02:54:44 UTC; biocbuild
VignetteBuilder: knitr
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DEXSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DEXSeq'
    finding HTML links ... done
    DEXSeq-defunct                          html  
    DEXSeq                                  html  
    DEXSeqDataSet                           html  
    DEXSeqHTML                              html  
    DEXSeqResults                           html  
    accessors                               html  
    counts                                  html  
    estimateDispersions                     html  
    estimateExonFoldChanges                 html  
    estimateSizeFactors                     html  
    methods-gr                              html  
Rd warning: /tmp/RtmptilW2d/R.INSTALL5f634fca0e3/DEXSeq/man/methods-gr.Rd:32: missing file link 'findOverlaps'
Rd warning: /tmp/RtmptilW2d/R.INSTALL5f634fca0e3/DEXSeq/man/methods-gr.Rd:36: missing file link 'findOverlaps'
    otherMethods                            html  
    perGeneQValue                           html  
    plotDEXSeq                              html  
    plotDispEsts                            html  
    plotMA                                  html  
    testForDEU                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEXSeq)
Making 'packages.html' ... done