Package: GenVisR
Title: Genomic Visualizations in R
Version: 1.39.0
Authors@R: c(person(given="Zachary", family="Skidmore", email="zlskidmore@gmail.com",
          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 <zlskidmore@gmail.com>
Description: Produce highly customizable publication quality graphics for
    genomic data primarily at the cohort level.
Depends: R (>= 3.3.0), methods
Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures,
         GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools,
         IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis,
         data.table, BSgenome, GenomeInfoDb, VariantAnnotation
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, rmarkdown, vdiffr, formatR,
          TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38
VignetteBuilder: knitr
RoxygenNote: 7.2.3
Encoding: UTF-8
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]
Collate:
    'AllGenerics.R'
    'Clinical-class.R'
    'GMS_Virtual-class.R'
    'GMS-class.R'
    'GMS_v4-class.R'
    'GenVisR.R'
    'Lolliplot-class.R'
    'MutSpectra-class.R'
    'MutationAnnotationFormat_Virtual-class.R'
    'MutationAnnotationFormat-class.R'
    'MutationAnnotationFormat_v1.0-class.R'
    'MutationAnnotationFormat_v2.0-class.R'
    'MutationAnnotationFormat_v2.1-class.R'
    'MutationAnnotationFormat_v2.2-class.R'
    'MutationAnnotationFormat_v2.3-class.R'
    'MutationAnnotationFormat_v2.4-class.R'
    'Rainfall-class.R'
    'VEP_Virtual-class.R'
    'VEP-class.R'
    'VEP_v88-class.R'
    'Waterfall-class.R'
    'cnFreq.R'
    'cnFreq_buildMain.R'
    'cnFreq_disjoin.R'
    'cnFreq_qual.R'
    'cnSpec.R'
    'cnSpec_buildMain.R'
    'cnSpec_qual.R'
    'cnView.R'
    'cnView_buildMain.R'
    'cnView_qual.R'
    'compIdent.R'
    'compIdent_bamRcnt.R'
    'compIdent_bamRcnt_qual.R'
    'compIdent_buildMain.R'
    'compIdent_format.R'
    'covBars.R'
    'covBars_buildMain.R'
    'covBars_qual.R'
    'deprecated.R'
    'genCov.R'
    'genCov_alignPlot.R'
    'genCov_assign_ggplotGrob_height.R'
    'genCov_assign_ggplotGrob_width.R'
    'genCov_buildCov.R'
    'genCov_buildTrack.R'
    'genCov_extr_ggplotGrob_height.R'
    'genCov_extr_ggplotGrob_width.R'
    'genCov_qual.R'
    'genCov_trackViz.R'
    'geneViz.R'
    'geneViz_Granges2dataframe.R'
    'geneViz_buildGene.R'
    'geneViz_calcGC.R'
    'geneViz_cdsFromTXID.R'
    'geneViz_extrCDS.R'
    'geneViz_extrUTR.R'
    'geneViz_formatUTR.R'
    'geneViz_formatcds.R'
    'geneViz_mapCoordSpace.R'
    'geneViz_mapCovCoordSpace.R'
    'geneViz_mergeRegions.R'
    'geneViz_mergeTypeRegions.R'
    'geneViz_mergeTypes.R'
    'ideoView.R'
    'ideoView_buildMain.R'
    'ideoView_formatCytobands.R'
    'ideoView_qual.R'
    'lohSpec.R'
    'lohSpec_buildMain.R'
    'lohSpec_fileGlob.R'
    'lohSpec_lohCalc.R'
    'lohSpec_qual.R'
    'lohSpec_slidingWindow.R'
    'lohSpec_stepCalc.R'
    'lohSpec_tileCalc.R'
    'lohSpec_tilePosition.R'
    'lohSpec_tileWindow.R'
    'lohSpec_windowPosition.R'
    'lohView.R'
    'lohView_buildMain.R'
    'lohView_qual.R'
    'multi_align.R'
    'multi_buildClin.R'
    'multi_chrBound.R'
    'multi_cytobandRet.R'
    'multi_selectOut.R'
    'multi_subsetChr.R'