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DESCRIPTION
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Package: GenVisR
Title: Genomic Visualizations in R
Version: 1.8.0
Authors@R: c(person(given="Zachary", family="Skidmore", email="[email protected]",
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="[email protected]", role="aut"), person(given="Obi", family="Griffith",
email="[email protected]", role="aut"), person(given="Malachi", family="Griffith",
email="[email protected]", role="aut"))
Maintainer: Zachary Skidmore <[email protected]>
Description: Produce highly customizable publication quality graphics for
genomic data primarily at the cohort level.
Depends: R (>= 3.3.0), methods
Imports: AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField, GenomicFeatures,
GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), grid, gridExtra, gtable, gtools,
IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats,
utils, viridis, data.table, BSgenome, grDevices, GenomeInfoDb
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
VignetteBuilder: knitr
RoxygenNote: 6.0.1.9000
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'
'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'
'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'
'lolliplot.R'
'lolliplot_AA2sidechain.R'
'lolliplot_Codon2AA.R'
'lolliplot_DNAconv.R'
'lolliplot_buildMain.R'
'lolliplot_constructGene.R'
'lolliplot_dodgeCoordX.R'
'lolliplot_dodgeCoordY.R'
'lolliplot_fetchDomain.R'
'lolliplot_mutationObs.R'
'lolliplot_qual.R'
'lolliplot_reduceLolli.R'
'lolliplot_transcriptID2codingSeq.R'
'multi_align.R'
'multi_buildClin.R'
'multi_chrBound.R'
'multi_cytobandRet.R'
'multi_selectOut.R'
'multi_subsetChr.R'