GenVisR: Genomic Visualizations in R

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Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.

Author
Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut], Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith [aut]
Date of publication
None
Maintainer
Zachary Skidmore <zlskidmore@gmail.com>
License
GPL-3 + file LICENSE
Version
1.2.0

View on Bioconductor

Man pages

brcaMAF
Truncated BRCA MAF file
cnFreq
Construct copy-number frequency plot
cnFreq_buildMain
Construct CN frequency plot
cnFreq_qual
check input to cnFreq
cnSpec
Construct copy-number cohort plot
cnSpec_buildMain
Construct CN cohort plot
cnSpec_qual
Construct CN cohort plot
cnView
Construct copy-number single sample plot
cnView_buildMain
construct CN plot
cnView_qual
check input to cnView
compIdent
Construct identity snp comparison plot
compIdent_bamRcnt
Count nucleotide reads at SNP locations
compIdent_bamRcnt_qual
Count nucleotide reads at SNP locations
compIdent_buildMain
Compare sample identities
compIdent_format
Format readcount tables from compIdent
covBars
Construct an overall coverage cohort plot
covBars_buildMain
Construct coverage cohort plot
covBars_qual
Construct coverage cohort plot
cytoGeno
Cytogenetic banding dataset
genCov
Construct a region of interest coverage plot
genCov_alignPlot
align plots on an axis
genCov_assign_ggplotGrob_height
assign ggplotGrob height
genCov_assign_ggplotGrob_width
assign ggplotGrob width
genCov_buildCov
build coverage plot
genCov_buildTrack
build label for plot
genCov_extr_ggplotGrob_height
extract ggplotGrob height
genCov_extr_ggplotGrob_width
extract ggplotGrob width
genCov_qual
Perform quality control on genCov data
genCov_trackViz
Overlay tracks with plots
geneViz
Construct a gene-features plot
geneViz_buildGene
build gene plot
geneViz_calcGC
Calculate GC content
geneViz_cdsFromTXID
cdsFromTXID
geneViz_extrCDS
Extract CDS
geneViz_extrUTR
Extract UTR
geneViz_formatCDS
format cds
geneViz_formatUTR
format UTR
geneViz_Granges2dataframe
Convert Granges object to dataframe
geneViz_mapCoordSpace
Map regions to transformed space
geneViz_mapCovCoordSpace
Map coverage track regions to transformed space
geneViz_mergeRegions
Create Region Table
geneViz_mergeTypeRegions
Create Typed Region Table
geneViz_mergeTypes
Merge Typed Region Tables
GenVisR
GenVisR
HCC1395_Germline
Germline Calls
HCC1395_N
Normal BAM
HCC1395_T
Tumor BAM
hg19chr
hg19 chromosome boundaries
ideoView
Construct an ideogram
ideoView_buildMain
build chromosome
ideoView_formatCytobands
reformat cytogenetic band data frame
ideoView_qual
Check input to ideoView
lohSpec
Plot LOH data
lohSpec_buildMain
Plot LOH data
lohSpec_fileGlob
Grab data for lohSpec
lohSpec_lohCalc
Calculate loh difference
lohSpec_qual
Check input to lohSpec
lohSpec_slidingWindow
Obtain LOH data
lohSpec_stepCalc
Obtain average loh within each step
lohSpec_tileCalc
Calculate loh difference
lohSpec_tilePosition
Obtain window information
lohSpec_tileWindow
Obtain LOH data
lohSpec_windowPosition
Obtain window information
lohView
Construct LOH chromosome plot
lohView_buildMain
construct loh plot
lohView_qual
check input to lohView
lolliplot
Construct a lolliplot
lolliplot_AA2sidechain
Convert AA to side chain classification
lolliplot_buildMain
Construct Lolliplot
lolliplot_Codon2AA
Convert Codon to AA
lolliplot_constructGene
Construct gene information
lolliplot_DNAconv
Convert DNA character string
lolliplot_dodgeCoordX
dodge coordinates
lolliplot_dodgeCoordY
dodge coordinates
lolliplot_fetchDomain
fetch protein domains
lolliplot_mutationObs
format mutation observations
lolliplot_qual
Check input to lolliplot
lolliplot_reduceLolli
Reduce Lolli
lolliplot_transcriptID2codingSeq
fetch protein length
LucCNseg
Truncated CN segments
multi_align
align CN/LOH plots on x axis
multi_buildClin
plot clinical information
multi_chrBound
retrieve and format CN_cohort plot supplemental data
multi_cytobandRet
Retrieve cytogenetic bands
multi_selectOut
Choose output
multi_subsetChr
subset based on chr
SNPloci
Identity snps
TvTi
Construct transition-transversion plot
TvTi_alignPlot
align TvTi plots on y axis
TvTi_annoTransTranv
Annotate Transitions and Transversions
TvTi_buildMain
build transitions/transversions
TvTi_calcTransTranvFreq
Calculate Transition/Transversion Frequency
TvTi_convMAF
Convert .maf format to internal format
TvTi_qual
Check input to TvTi
TvTi_rmIndel
Remove indels
TvTi_rmMnuc
Remove multinucleotide codes
waterfall
Construct a waterfall plot
waterfall_align
align plots
waterfall_buildGenePrevelance
plot mutation recurrence in genes
waterfall_buildMain
Plot a mutation heatmap
waterfall_buildMutBurden_A
plot mutation burden
waterfall_buildMutBurden_B
plot mutation burden
waterfall_calcMutFreq
Calculate Synonymous/Nonsynonymous mutation frequency
waterfall_Custom2anno
Convert Custom File
waterfall_geneAlt
mutation sample cutoff gene based
waterfall_geneRecurCutoff
Mutation Recurrence Cutoff
waterfall_geneSort
sort waterfall file by gene
waterfall_hierarchyTRV
Hiearchical removal of MAF entries
waterfall_MAF2anno
Convert MAF File
waterfall_MGI2anno
Convert MGI File
waterfall_NA2gene
Assign NA samples a gene
waterfall_qual
Check input to mutSpec
waterfall_rmvSilent
Silent Mutation Removal
waterfall_sampAlt
mutation sample subset sample based
waterfall_sampSort
sort samples in an internal waterfall file.

Files in this package

GenVisR/DESCRIPTION
GenVisR/LICENSE
GenVisR/NAMESPACE
GenVisR/NEWS
GenVisR/R
GenVisR/R/GenVisR.R
GenVisR/R/TvTi.R
GenVisR/R/TvTi_alignPlot.R
GenVisR/R/TvTi_annoTransTranv.R
GenVisR/R/TvTi_buildMain.R
GenVisR/R/TvTi_calcTransTranvFreq.R
GenVisR/R/TvTi_convMaf.R
GenVisR/R/TvTi_qual.R
GenVisR/R/TvTi_rmIndel.R
GenVisR/R/TvTi_rmMnuc.R
GenVisR/R/cnFreq.R
GenVisR/R/cnFreq_buildMain.R
GenVisR/R/cnFreq_qual.R
GenVisR/R/cnSpec.R
GenVisR/R/cnSpec_buildMain.R
GenVisR/R/cnSpec_qual.R
GenVisR/R/cnView.R
GenVisR/R/cnView_buildMain.R
GenVisR/R/cnView_qual.R
GenVisR/R/compIdent.R
GenVisR/R/compIdent_bamRcnt.R
GenVisR/R/compIdent_bamRcnt_qual.R
GenVisR/R/compIdent_buildMain.R
GenVisR/R/compIdent_format.R
GenVisR/R/covBars.R
GenVisR/R/covBars_buildMain.R
GenVisR/R/covBars_qual.R
GenVisR/R/genCov.R
GenVisR/R/genCov_alignPlot.R
GenVisR/R/genCov_assign_ggplotGrob_height.R
GenVisR/R/genCov_assign_ggplotGrob_width.R
GenVisR/R/genCov_buildCov.R
GenVisR/R/genCov_buildTrack.R
GenVisR/R/genCov_extr_ggplotGrob_height.R
GenVisR/R/genCov_extr_ggplotGrob_width.R
GenVisR/R/genCov_qual.R
GenVisR/R/genCov_trackViz.R
GenVisR/R/geneViz.R
GenVisR/R/geneViz_Granges2dataframe.R
GenVisR/R/geneViz_buildGene.R
GenVisR/R/geneViz_calcGC.R
GenVisR/R/geneViz_cdsFromTXID.R
GenVisR/R/geneViz_extrCDS.R
GenVisR/R/geneViz_extrUTR.R
GenVisR/R/geneViz_formatUTR.R
GenVisR/R/geneViz_formatcds.R
GenVisR/R/geneViz_mapCoordSpace.R
GenVisR/R/geneViz_mapCovCoordSpace.R
GenVisR/R/geneViz_mergeRegions.R
GenVisR/R/geneViz_mergeTypeRegions.R
GenVisR/R/geneViz_mergeTypes.R
GenVisR/R/ideoView.R
GenVisR/R/ideoView_buildMain.R
GenVisR/R/ideoView_formatCytobands.R
GenVisR/R/ideoView_qual.R
GenVisR/R/lohSpec.R
GenVisR/R/lohSpec_buildMain.R
GenVisR/R/lohSpec_fileGlob.R
GenVisR/R/lohSpec_lohCalc.R
GenVisR/R/lohSpec_qual.R
GenVisR/R/lohSpec_slidingWindow.R
GenVisR/R/lohSpec_stepCalc.R
GenVisR/R/lohSpec_tileCalc.R
GenVisR/R/lohSpec_tilePosition.R
GenVisR/R/lohSpec_tileWindow.R
GenVisR/R/lohSpec_windowPosition.R
GenVisR/R/lohView.R
GenVisR/R/lohView_buildMain.R
GenVisR/R/lohView_qual.R
GenVisR/R/lolliplot.R
GenVisR/R/lolliplot_AA2sidechain.R
GenVisR/R/lolliplot_Codon2AA.R
GenVisR/R/lolliplot_DNAconv.R
GenVisR/R/lolliplot_buildMain.R
GenVisR/R/lolliplot_constructGene.R
GenVisR/R/lolliplot_dodgeCoordX.R
GenVisR/R/lolliplot_dodgeCoordY.R
GenVisR/R/lolliplot_fetchDomain.R
GenVisR/R/lolliplot_mutationObs.R
GenVisR/R/lolliplot_qual.R
GenVisR/R/lolliplot_reduceLolli.R
GenVisR/R/lolliplot_transcriptID2codingSeq.R
GenVisR/R/multi_align.R
GenVisR/R/multi_buildClin.R
GenVisR/R/multi_chrBound.R
GenVisR/R/multi_cytobandRet.R
GenVisR/R/multi_selectOut.R
GenVisR/R/multi_subsetChr.R
GenVisR/R/waterfall.R
GenVisR/R/waterfall_Custom2anno.R
GenVisR/R/waterfall_MAF2anno.R
GenVisR/R/waterfall_MGI2anno.R
GenVisR/R/waterfall_NA2gene.R
GenVisR/R/waterfall_align.R
GenVisR/R/waterfall_buildGenePrevelance.R
GenVisR/R/waterfall_buildMain.R
GenVisR/R/waterfall_buildMutBurden_A.R
GenVisR/R/waterfall_buildMutBurden_B.R
GenVisR/R/waterfall_calcMutFreq.R
GenVisR/R/waterfall_geneAlt.R
GenVisR/R/waterfall_geneRecurCutoff.R
GenVisR/R/waterfall_geneSort.R
GenVisR/R/waterfall_hierarchyTRV.R
GenVisR/R/waterfall_qual.R
GenVisR/R/waterfall_rmvSilent.R
GenVisR/R/waterfall_sampAlt.R
GenVisR/R/waterfall_sampSort.R
GenVisR/README.md
GenVisR/build
GenVisR/build/vignette.rds
GenVisR/data
GenVisR/data/HCC1395_Germline.rda
GenVisR/data/HCC1395_N.rda
GenVisR/data/HCC1395_T.rda
GenVisR/data/LucCNseg.rda
GenVisR/data/SNPloci.rda
GenVisR/data/brcaMAF.rda
GenVisR/data/cytoGeno.rda
GenVisR/data/hg19chr.rda
GenVisR/inst
GenVisR/inst/CITATION
GenVisR/inst/doc
GenVisR/inst/doc/GenVisR_intro.R
GenVisR/inst/doc/GenVisR_intro.Rmd
GenVisR/inst/doc/GenVisR_intro.html
GenVisR/inst/doc/waterfall_introduction.R
GenVisR/inst/doc/waterfall_introduction.Rmd
GenVisR/inst/doc/waterfall_introduction.html
GenVisR/man
GenVisR/man/GenVisR.Rd
GenVisR/man/HCC1395_Germline.Rd
GenVisR/man/HCC1395_N.Rd
GenVisR/man/HCC1395_T.Rd
GenVisR/man/LucCNseg.Rd
GenVisR/man/SNPloci.Rd
GenVisR/man/TvTi.Rd
GenVisR/man/TvTi_alignPlot.Rd
GenVisR/man/TvTi_annoTransTranv.Rd
GenVisR/man/TvTi_buildMain.Rd
GenVisR/man/TvTi_calcTransTranvFreq.Rd
GenVisR/man/TvTi_convMAF.Rd
GenVisR/man/TvTi_qual.Rd
GenVisR/man/TvTi_rmIndel.Rd
GenVisR/man/TvTi_rmMnuc.Rd
GenVisR/man/brcaMAF.Rd
GenVisR/man/cnFreq.Rd
GenVisR/man/cnFreq_buildMain.Rd
GenVisR/man/cnFreq_qual.Rd
GenVisR/man/cnSpec.Rd
GenVisR/man/cnSpec_buildMain.Rd
GenVisR/man/cnSpec_qual.Rd
GenVisR/man/cnView.Rd
GenVisR/man/cnView_buildMain.Rd
GenVisR/man/cnView_qual.Rd
GenVisR/man/compIdent.Rd
GenVisR/man/compIdent_bamRcnt.Rd
GenVisR/man/compIdent_bamRcnt_qual.Rd
GenVisR/man/compIdent_buildMain.Rd
GenVisR/man/compIdent_format.Rd
GenVisR/man/covBars.Rd
GenVisR/man/covBars_buildMain.Rd
GenVisR/man/covBars_qual.Rd
GenVisR/man/cytoGeno.Rd
GenVisR/man/genCov.Rd
GenVisR/man/genCov_alignPlot.Rd
GenVisR/man/genCov_assign_ggplotGrob_height.Rd
GenVisR/man/genCov_assign_ggplotGrob_width.Rd
GenVisR/man/genCov_buildCov.Rd
GenVisR/man/genCov_buildTrack.Rd
GenVisR/man/genCov_extr_ggplotGrob_height.Rd
GenVisR/man/genCov_extr_ggplotGrob_width.Rd
GenVisR/man/genCov_qual.Rd
GenVisR/man/genCov_trackViz.Rd
GenVisR/man/geneViz.Rd
GenVisR/man/geneViz_Granges2dataframe.Rd
GenVisR/man/geneViz_buildGene.Rd
GenVisR/man/geneViz_calcGC.Rd
GenVisR/man/geneViz_cdsFromTXID.Rd
GenVisR/man/geneViz_extrCDS.Rd
GenVisR/man/geneViz_extrUTR.Rd
GenVisR/man/geneViz_formatCDS.Rd
GenVisR/man/geneViz_formatUTR.Rd
GenVisR/man/geneViz_mapCoordSpace.Rd
GenVisR/man/geneViz_mapCovCoordSpace.Rd
GenVisR/man/geneViz_mergeRegions.Rd
GenVisR/man/geneViz_mergeTypeRegions.Rd
GenVisR/man/geneViz_mergeTypes.Rd
GenVisR/man/hg19chr.Rd
GenVisR/man/ideoView.Rd
GenVisR/man/ideoView_buildMain.Rd
GenVisR/man/ideoView_formatCytobands.Rd
GenVisR/man/ideoView_qual.Rd
GenVisR/man/lohSpec.Rd
GenVisR/man/lohSpec_buildMain.Rd
GenVisR/man/lohSpec_fileGlob.Rd
GenVisR/man/lohSpec_lohCalc.Rd
GenVisR/man/lohSpec_qual.Rd
GenVisR/man/lohSpec_slidingWindow.Rd
GenVisR/man/lohSpec_stepCalc.Rd
GenVisR/man/lohSpec_tileCalc.Rd
GenVisR/man/lohSpec_tilePosition.Rd
GenVisR/man/lohSpec_tileWindow.Rd
GenVisR/man/lohSpec_windowPosition.Rd
GenVisR/man/lohView.Rd
GenVisR/man/lohView_buildMain.Rd
GenVisR/man/lohView_qual.Rd
GenVisR/man/lolliplot.Rd
GenVisR/man/lolliplot_AA2sidechain.Rd
GenVisR/man/lolliplot_Codon2AA.Rd
GenVisR/man/lolliplot_DNAconv.Rd
GenVisR/man/lolliplot_buildMain.Rd
GenVisR/man/lolliplot_constructGene.Rd
GenVisR/man/lolliplot_dodgeCoordX.Rd
GenVisR/man/lolliplot_dodgeCoordY.Rd
GenVisR/man/lolliplot_fetchDomain.Rd
GenVisR/man/lolliplot_mutationObs.Rd
GenVisR/man/lolliplot_qual.Rd
GenVisR/man/lolliplot_reduceLolli.Rd
GenVisR/man/lolliplot_transcriptID2codingSeq.Rd
GenVisR/man/multi_align.Rd
GenVisR/man/multi_buildClin.Rd
GenVisR/man/multi_chrBound.Rd
GenVisR/man/multi_cytobandRet.Rd
GenVisR/man/multi_selectOut.Rd
GenVisR/man/multi_subsetChr.Rd
GenVisR/man/waterfall.Rd
GenVisR/man/waterfall_Custom2anno.Rd
GenVisR/man/waterfall_MAF2anno.Rd
GenVisR/man/waterfall_MGI2anno.Rd
GenVisR/man/waterfall_NA2gene.Rd
GenVisR/man/waterfall_align.Rd
GenVisR/man/waterfall_buildGenePrevelance.Rd
GenVisR/man/waterfall_buildMain.Rd
GenVisR/man/waterfall_buildMutBurden_A.Rd
GenVisR/man/waterfall_buildMutBurden_B.Rd
GenVisR/man/waterfall_calcMutFreq.Rd
GenVisR/man/waterfall_geneAlt.Rd
GenVisR/man/waterfall_geneRecurCutoff.Rd
GenVisR/man/waterfall_geneSort.Rd
GenVisR/man/waterfall_hierarchyTRV.Rd
GenVisR/man/waterfall_qual.Rd
GenVisR/man/waterfall_rmvSilent.Rd
GenVisR/man/waterfall_sampAlt.Rd
GenVisR/man/waterfall_sampSort.Rd
GenVisR/tests
GenVisR/tests/testthat
GenVisR/tests/testthat.R
GenVisR/tests/testthat/test-TvTi.R
GenVisR/tests/testthat/test-TvTi_calcTransTranvFreq.R
GenVisR/tests/testthat/test-TvTi_convMaf.R
GenVisR/tests/testthat/test-TvTi_qual.R
GenVisR/tests/testthat/test-TvTi_rmIndel.R
GenVisR/tests/testthat/test-TvTi_rmMnuc.R
GenVisR/tests/testthat/test-cnSpec.R
GenVisR/tests/testthat/test-cnSpec_qual.R
GenVisR/tests/testthat/test-cnView_qual.R
GenVisR/tests/testthat/test-genCov_qual.R
GenVisR/tests/testthat/test-ideoView_formatCytobands.R
GenVisR/tests/testthat/test-lolliplot_AA2sidechain.R
GenVisR/tests/testthat/test-lolliplot_Codon2AA.R
GenVisR/tests/testthat/test-lolliplot_DNAconv.R
GenVisR/tests/testthat/test-lolliplot_constructGene.R
GenVisR/tests/testthat/test-lolliplot_dodgeCoordX.R
GenVisR/tests/testthat/test-lolliplot_dodgeCoordY.R
GenVisR/tests/testthat/test-lolliplot_mutationObs.R
GenVisR/tests/testthat/test-lolliplot_qual.R
GenVisR/tests/testthat/test-lolliplot_reduceLolli.R
GenVisR/tests/testthat/test-multi_chrBound.R
GenVisR/tests/testthat/test-multi_cytobandRet.R
GenVisR/tests/testthat/test-multi_subsetChr.R
GenVisR/tests/testthat/test-waterfall.R
GenVisR/tests/testthat/test-waterfall_MAF2anno.R
GenVisR/tests/testthat/test-waterfall_MGI2anno.R
GenVisR/tests/testthat/test-waterfall_NA2gene.R
GenVisR/tests/testthat/test-waterfall_calcMutFreq.R
GenVisR/tests/testthat/test-waterfall_geneAlt.R
GenVisR/tests/testthat/test-waterfall_geneRecurCutoff.R
GenVisR/tests/testthat/test-waterfall_geneSort.R
GenVisR/tests/testthat/test-waterfall_qual.R
GenVisR/tests/testthat/test-waterfall_rmvSilent.R
GenVisR/tests/testthat/test-waterfall_sampAlt.R
GenVisR/tests/testthat/test-waterfall_sampSort.R
GenVisR/tests/testthat/test_waterfall_hierarchyTRV.R
GenVisR/vignettes
GenVisR/vignettes/GenVisR_intro.Rmd
GenVisR/vignettes/waterfall_introduction.Rmd