ballgown

Package: ballgown
Maintainer: Jack Fu <jmfu@jhsph.edu>
Authors@R: c(person("Jack", "Fu", role=c("aut"), email="jmfu@jhsph.edu"),
person(c("Alyssa", "C."), "Frazee", role=c("aut", "cre"),
email="alyssa.frazee@gmail.com"), person("Leonardo", "Collado-Torres",
role=c("aut"), email="lcollado@jhu.edu"), person(c("Andrew", "E."),
"Jaffe", role=c("aut")), person(c("Jeffrey", "T."), "Leek", role=c("aut",
"ths"), email="jtleek@gmail.com"))
Version: 2.4.2
License: Artistic-2.0
Title: Flexible, isoform-level differential expression analysis
Description: Tools for statistical analysis of assembled transcriptomes,
including flexible differential expression analysis, visualization of
transcript structures, and matching of assembled transcripts to annotation.
Depends: R (>= 3.1.1), methods
Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors
(>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>=
1.29.25), Biobase (>= 2.25.0), GenomeInfoDb
Suggests: testthat, knitr
VignetteBuilder: knitr
BugReports: https://github.com/alyssafrazee/ballgown/issues
biocViews: RNASeq, StatisticalMethod, Preprocessing,
DifferentialExpression
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 04:43:26 UTC; biocbuild
Author: Jack Fu [aut],
Alyssa C. Frazee [aut, cre],
Leonardo Collado-Torres [aut],
Andrew E. Jaffe [aut],
Jeffrey T. Leek [aut, ths]

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ballgown' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'structure' in package 'ballgown'
** help
*** installing help indices
  converting help for package 'ballgown'
    finding HTML links ... done
    annotate_assembly                       html  
    ballgown-class                          html  
    ballgown-constructor                    html  
    ballgown-package                        html  
    ballgownrsem                            html  
    bg                                      html  
    checkAssembledTx                        html  
    clusterTranscripts                      html  
    collapseTranscripts                     html  
    contains                                html  
    dirs                                    html  
    eexpr                                   html  
    expr-replace                            html  
    expr                                    html  
    exprfilter                              html  
    geneIDs                                 html  
    geneNames                               html  
    getAttributeField                       html  
    getGenes                                html  
    gexpr                                   html  
    gffRead                                 html  
    gffReadGR                               html  
    iexpr                                   html  
    indexes-replace                         html  
    indexes                                 html  
    last                                    html  
    mergedDate                              html  
    pData-replace                           html  
    pData                                   html  
    pctOverlap                              html  
    plotLatentTranscripts                   html  
    plotMeans                               html  
    plotTranscripts                         html  
    sampleNames                             html  
    seqnames                                html  
    stattest                                html  
    structure                               html  
    subset                                  html  
    tGene                                   html  
    texpr                                   html  
    transcriptIDs                           html  
    transcriptNames                         html  
    writeFiles                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ballgown)
Making 'packages.html' ... done