CompGO

Package: CompGO
Title: An R pipeline for .bed file annotation, comparing GO term
enrichment between gene sets and data visualisation
Description: This package contains functions to accomplish several tasks. It is
able to download full genome databases from UCSC, import .bed files easily,
annotate these .bed file regions with genes (plus distance) from
aforementioned database dumps, interface with DAVID to create functional
annotation and gene ontology enrichment charts based on gene lists (such as
those generated from input .bed files) and finally visualise and compare
these enrichments using either directed acyclic graphs or scatterplots.
Version: 1.8.0
Authors@R: c(person("Sam D.", "Bassett", role = 'aut',
email='S.Bassett@victorchang.edu.au'),
person("Ashley J.", "Waardenberg", role=c('aut', 'cre'),
email='A.Waardenberg@victorchang.edu.au'))
License: GPL-2
Depends: RDAVIDWebService
Imports: rtracklayer, Rgraphviz, ggplot2, GenomicFeatures,
TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2,
pathview
biocViews: GeneSetEnrichment, MultipleComparison, GO, Visualization
NeedsCompilation: no
Packaged: 2016-05-04 05:23:46 UTC; biocbuild
Author: Sam D. Bassett [aut],
Ashley J. Waardenberg [aut, cre]
Maintainer: Ashley J. Waardenberg <A.Waardenberg@victorchang.edu.au>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'CompGO' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CompGO'
    finding HTML links ... done
    PCAplot                                 html  
    annotateBedFromDb                       html  
    bed.sample                              html  
    compareZscores                          html  
    doZtrans.single                         html  
    gata4                                   html  
    getFnAnot_genome                        html  
    mef2a                                   html  
    nkx25                                   html  
    p300                                    html  
    plotDendrogram                          html  
    plotInteractive                         html  
    plotPairwise                            html  
    plotTwoGODags                           html  
    plotZRankedDAG                          html  
    plotZScores                             html  
    slidingJaccard                          html  
    srf                                     html  
    tbx5                                    html  
    viewKegg                                html  
    zTransformDirectory                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CompGO)
Making 'packages.html' ... done