GenVisR

Package: GenVisR
Title: Genomic Visualizations in R
Version: 1.0.4
Authors@R: c(person(given="Zachary", family="Skidmore", email="zskidmor@genome.wustl.edu",
role=c("aut", "cre")), person(given="Alex", family="Wagner", role="aut"),
person(given="Robert", family="Lesurf", role="aut"), person(given="Katie",
family="Campbell", role="aut"), person(given="Jason", family="Kunisaki",
email="kunisakijh@gmail.com", role="aut"), person(given="Obi", family="Griffith",
email="ogriffit@genome.wustl.edu", role="aut"), person(given="Malachi", family="Griffith",
email="mgriffit@genome.wustl.edu", role="aut"))
Maintainer: Zachary Skidmore <zskidmor@genome.wustl.edu>
Description: Produce highly customizable publication quality graphics for genomic data
primarily at the cohort level.
Depends: R (>= 3.3.0)
Imports: AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField,
GenomicFeatures, GenomicRanges, ggplot2 (>= 0.9.2), grid,
gridExtra, gtable, gtools, IRanges, plyr (>= 1.8.3), reshape2,
Rsamtools, scales, stats, utils, viridis
License: GPL-3 + file LICENSE
BugReports: https://github.com/griffithlab/GenVisR/issues
biocViews: Infrastructure, DataRepresentation, Classification, DNASeq
LazyData: true
Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL,
roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Author: Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut], Katie Campbell
[aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith [aut]
Packaged: 2016-06-14 05:48:57 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenVisR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenVisR'
    finding HTML links ... done
    GenVisR                                 html  
    HCC1395_Germline                        html  
    HCC1395_N                               html  
    HCC1395_T                               html  
    LucCNseg                                html  
    SNPloci                                 html  
    TvTi                                    html  
    TvTi_alignPlot                          html  
    TvTi_annoTransTranv                     html  
    TvTi_buildMain                          html  
    TvTi_calcTransTranvFreq                 html  
    TvTi_convMAF                            html  
    TvTi_qual                               html  
    TvTi_rmIndel                            html  
    TvTi_rmMnuc                             html  
    brcaMAF                                 html  
    cnFreq                                  html  
    cnFreq_buildMain                        html  
    cnFreq_qual                             html  
    cnSpec                                  html  
    cnSpec_buildMain                        html  
    cnSpec_qual                             html  
    cnView                                  html  
    cnView_buildMain                        html  
    cnView_qual                             html  
    compIdent                               html  
    compIdent_bamRcnt                       html  
    compIdent_bamRcnt_qual                  html  
    compIdent_buildMain                     html  
    compIdent_format                        html  
    covBars                                 html  
    covBars_buildMain                       html  
    covBars_qual                            html  
    cytoGeno                                html  
    genCov                                  html  
    genCov_alignPlot                        html  
    genCov_assign_ggplotGrob_height         html  
    genCov_assign_ggplotGrob_width          html  
    genCov_buildCov                         html  
    genCov_buildTrack                       html  
    genCov_extr_ggplotGrob_height           html  
    genCov_extr_ggplotGrob_width            html  
    genCov_qual                             html  
    genCov_trackViz                         html  
    geneViz                                 html  
    geneViz_Granges2dataframe               html  
    geneViz_buildGene                       html  
    geneViz_calcGC                          html  
    geneViz_cdsFromTXID                     html  
    geneViz_extrCDS                         html  
    geneViz_extrUTR                         html  
    geneViz_formatCDS                       html  
    geneViz_formatUTR                       html  
    geneViz_mapCoordSpace                   html  
    geneViz_mapCovCoordSpace                html  
    geneViz_mergeRegions                    html  
    geneViz_mergeTypeRegions                html  
    geneViz_mergeTypes                      html  
    hg19chr                                 html  
    ideoView                                html  
    ideoView_buildMain                      html  
    ideoView_formatCytobands                html  
    ideoView_qual                           html  
    lohSpec                                 html  
    lohSpec_buildMain                       html  
    lohSpec_fileGlob                        html  
    lohSpec_lohCalc                         html  
    lohSpec_qual                            html  
    lohSpec_slidingWindow                   html  
    lohSpec_stepCalc                        html  
    lohSpec_tileCalc                        html  
    lohSpec_tilePosition                    html  
    lohSpec_tileWindow                      html  
    lohSpec_windowPosition                  html  
    lohView                                 html  
    lohView_buildMain                       html  
    lohView_qual                            html  
    lolliplot                               html  
    lolliplot_AA2sidechain                  html  
    lolliplot_Codon2AA                      html  
    lolliplot_DNAconv                       html  
    lolliplot_buildMain                     html  
    lolliplot_constructGene                 html  
    lolliplot_dodgeCoordX                   html  
    lolliplot_dodgeCoordY                   html  
    lolliplot_fetchDomain                   html  
    lolliplot_mutationObs                   html  
    lolliplot_qual                          html  
    lolliplot_reduceLolli                   html  
    lolliplot_transcriptID2codingSeq        html  
    multi_align                             html  
    multi_buildClin                         html  
    multi_chrBound                          html  
    multi_cytobandRet                       html  
    multi_selectOut                         html  
    multi_subsetChr                         html  
    waterfall                               html  
    waterfall_Custom2anno                   html  
    waterfall_MAF2anno                      html  
    waterfall_MGI2anno                      html  
    waterfall_NA2gene                       html  
    waterfall_align                         html  
    waterfall_buildGenePrevelance           html  
    waterfall_buildMain                     html  
    waterfall_buildMutBurden_A              html  
    waterfall_buildMutBurden_B              html  
    waterfall_calcMutFreq                   html  
    waterfall_geneAlt                       html  
    waterfall_geneRecurCutoff               html  
    waterfall_geneSort                      html  
    waterfall_hierarchyTRV                  html  
    waterfall_qual                          html  
    waterfall_rmvSilent                     html  
    waterfall_sampAlt                       html  
    waterfall_sampSort                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenVisR)
Making 'packages.html' ... done