GenVisR
Genomic Visualizations in R

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Genomic Visualizations in R

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tests/testthat.R
tests/figs/deps.txt
tests/figs/waterfall-final-plot/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
tests/figs/waterfall-final-plot/final-waterfall-and-top-sub-plot-alter-sectionheights.svg
tests/figs/waterfall-final-plot/final-waterfall-base.svg
tests/figs/waterfall-final-plot/final-waterfall-and-left-sub-plot.svg
tests/figs/waterfall-final-plot/final-waterfall-and-top-sub-plot.svg
tests/figs/waterfall-final-plot/final-waterfall-and-top-and-left-sub-plot.svg
tests/figs/waterfall-final-plot/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
tests/figs/lolliplotplots-constructor/lolliplot-plot-base.svg
tests/figs/lolliplotplots-constructor/lolliplot-plot-base-add-labels.svg
tests/figs/lolliplotplots-constructor/lolliplot-plot-base-add-domain-palette.svg
tests/figs/lolliplotplots-constructor/lolliplot-plot-base-add-mutation-palette.svg
tests/figs/lolliplotplots-constructor/lolliplot-density-plot.svg
tests/figs/lolliplotplots-constructor/lolliplot-density-plot-layer.svg
tests/figs/lolliplotplots-constructor/lolliplot-plot-base-add-layer.svg
tests/figs/mutspectra-proportion-plot/mutspectra-proportion-plot-custom-pallette.svg
tests/figs/mutspectra-proportion-plot/mutspectra-proportion-plot.svg
tests/figs/mutspectra-proportion-plot/mutspectra-proportion-plot-add-layer.svg
tests/figs/waterfall-mutation-plot/mutation-plot-add-layers.svg
tests/figs/waterfall-mutation-plot/mutation-plot-frequency-simple.svg
tests/figs/waterfall-mutation-plot/mutation-plot-burden-simple.svg
tests/figs/waterfall-mutation-plot/mutation-plot-frequency-complex.svg
tests/figs/waterfall-mutation-plot/mutation-plot-burden-complex.svg
tests/figs/mutspectra-final-plot/mutspectra-clinical.svg
tests/figs/mutspectra-final-plot/final-mutspectra-base.svg
tests/figs/mutspectra-final-plot/drawplot-mutspectra.svg
tests/figs/mutspectra-final-plot/final-mutspectra-alter-section-heights.svg
tests/figs/rainfall-density-plot/density-main-plot.svg
tests/figs/rainfall-density-plot/density-plot-add-layer.svg
tests/figs/rainfall-main-plot/rainfall-main-plot.svg
tests/figs/rainfall-main-plot/rainfall-plot-add-layer.svg
tests/figs/rainfall-main-plot/rainfall-plot-aesthetic-options.svg
tests/figs/rainfall-final-plot/final-rainfall-base.svg
tests/figs/rainfall-final-plot/drawplot-rainfall.svg
tests/figs/rainfall-final-plot/final-rainfall-alter-section-hieghts.svg
tests/figs/waterfall-constructor/drawplot-waterfall.svg
tests/figs/waterfall-constructor/addgene-waterfall.svg
tests/figs/waterfall-main-plot/main-waterfall-add-layers.svg
tests/figs/waterfall-main-plot/main-waterfall-plot-xtitle-false.svg
tests/figs/waterfall-main-plot/main-waterfall-plot-base.svg
tests/figs/waterfall-main-plot/main-waterfall-plot-grid-true.svg
tests/figs/waterfall-main-plot/main-waterfall-plot-label.svg
tests/figs/waterfall-main-plot/main-waterfall-plot-samplenames-false.svg
tests/figs/waterfall-main-plot/main-waterfall-plot-drop-true.svg
tests/figs/waterfall-gene-plot/gene-plot-proportion-complex.svg
tests/figs/waterfall-gene-plot/gene-plot-add-layers.svg
tests/figs/waterfall-gene-plot/gene-plot-proportion-simple.svg
tests/figs/waterfall-gene-plot/gene-plot-frequency-complex.svg
tests/figs/waterfall-gene-plot/gene-plot-frequency-simple.svg
tests/figs/lolliplot-final-plot/final-lolliplot-alter-section-height.svg
tests/figs/lolliplot-final-plot/final-lolliplot-base.svg
tests/figs/mutspectra-frequency-plot/mutspectra-frequency-plot-custom-pallette.svg
tests/figs/mutspectra-frequency-plot/mutspectra-frequency-plot.svg
tests/figs/mutspectra-frequency-plot/mutspectra-frequency-plot-add-layer.svg
tests/figs/lolliplot-accessors/drawplot-lolliplot.svg
tests/testthat/test-cnSpec.R tests/testthat/test-VEP-class.R tests/testthat/test-multi_chrBound.R tests/testthat/test-Lolliplot-class.R tests/testthat/test-cnSpec_qual.R tests/testthat/test-Rainfall-class.R tests/testthat/test-MutSpectra-class.R tests/testthat/test-multi_cytobandRet.R tests/testthat/test-deprecated.R tests/testthat/test-Waterfall-class.R tests/testthat/test-MutationAnnotationFormat-class.R tests/testthat/test-GMS-class.R tests/testthat/test-genCov_qual.R tests/testthat/test-ideoView_formatCytobands.R tests/testthat/test-multi_subsetChr.R tests/testthat/test-cnView_qual.R R/geneViz_extrUTR.R R/Lolliplot-class.R R/lohSpec_windowPosition.R R/GMS-class.R R/geneViz_mergeRegions.R R/covBars_buildMain.R R/ideoView_buildMain.R R/compIdent_buildMain.R R/GenVisR.R R/MutationAnnotationFormat_v2.4-class.R R/lohSpec_tilePosition.R R/cnView_buildMain.R R/deprecated.R R/cnFreq.R R/MutationAnnotationFormat_v2.1-class.R R/multi_cytobandRet.R R/lohSpec_stepCalc.R R/cnView_qual.R R/multi_buildClin.R R/Rainfall-class.R R/compIdent.R R/GMS_v4-class.R R/geneViz_mapCoordSpace.R R/compIdent_bamRcnt.R R/lohSpec_tileWindow.R R/multi_selectOut.R R/genCov_qual.R R/geneViz_buildGene.R R/lohView.R R/covBars.R R/VEP-class.R R/lohView_qual.R R/cnFreq_qual.R R/geneViz_calcGC.R R/multi_subsetChr.R R/covBars_qual.R R/ideoView_qual.R R/geneViz_extrCDS.R R/GMS_Virtual-class.R R/genCov_assign_ggplotGrob_height.R R/MutationAnnotationFormat_v2.0-class.R R/AllGenerics.R R/lohSpec.R R/genCov.R R/ideoView_formatCytobands.R R/geneViz_formatUTR.R R/genCov_alignPlot.R R/MutSpectra-class.R R/geneViz_mergeTypes.R R/lohSpec_slidingWindow.R R/compIdent_bamRcnt_qual.R R/geneViz_cdsFromTXID.R R/ideoView.R R/cnFreq_disjoin.R R/lohSpec_lohCalc.R R/VEP_Virtual-class.R R/geneViz_Granges2dataframe.R R/lohSpec_qual.R R/lohSpec_fileGlob.R R/lohSpec_buildMain.R R/geneViz_mapCovCoordSpace.R R/genCov_trackViz.R R/genCov_extr_ggplotGrob_height.R R/cnView.R R/compIdent_format.R R/geneViz.R R/MutationAnnotationFormat_v1.0-class.R R/MutationAnnotationFormat_Virtual-class.R R/MutationAnnotationFormat_v2.3-class.R R/MutationAnnotationFormat_v2.2-class.R R/genCov_buildCov.R R/genCov_extr_ggplotGrob_width.R R/cnSpec.R R/Clinical-class.R R/cnSpec_qual.R R/geneViz_formatcds.R R/cnFreq_buildMain.R R/MutationAnnotationFormat-class.R R/Waterfall-class.R R/VEP_v88-class.R R/multi_chrBound.R R/cnSpec_buildMain.R R/geneViz_mergeTypeRegions.R R/genCov_assign_ggplotGrob_width.R R/lohSpec_tileCalc.R R/multi_align.R R/genCov_buildTrack.R R/lohView_buildMain.R man/covBars.Rd man/drawPlot-methods.Rd man/cnView.Rd man/getSample-methods.Rd man/getData-methods.Rd man/MutationAnnotationFormat_Virtual-class.Rd man/Rainfall-class.Rd man/PIK3CA.Rd man/HCC1395_T.Rd man/MutSpectra-class.Rd man/HCC1395_N.Rd man/lolliplot.Rd man/hg19chr.Rd man/getDescription-methods.Rd man/getPath-methods.Rd man/VEP_v88-class.Rd man/genCov.Rd man/cnSpec.Rd man/MutationAnnotationFormat-class.Rd man/getHeader-methods.Rd man/GMS_Virtual-class.Rd man/waterfall.Rd man/LucCNseg.Rd man/VEP-class.Rd man/getPosition-methods.Rd man/geneViz.Rd man/MutationAnnotationFormat_v1.0-class.Rd man/GMS-class.Rd man/getVersion-methods.Rd man/Lolliplot-class.Rd man/MutationAnnotationFormat_v2.3-class.Rd man/TvTi.Rd man/VEP_Virtual-class.Rd man/lolliplot_AA2sidechain.Rd man/brcaMAF.Rd man/SNPloci.Rd man/Clinical-class.Rd man/cnFreq.Rd man/MutationAnnotationFormat_v2.4-class.Rd man/HCC1395_Germline.Rd man/MutationAnnotationFormat_v2.0-class.Rd man/GMS_v4-class.Rd man/Waterfall-class.Rd man/MutationAnnotationFormat_v2.1-class.Rd man/lohView.Rd man/getMutation-methods.Rd man/lolliplot_buildMain.Rd man/GenVisR.Rd man/compIdent.Rd man/writeData-methods.Rd man/getGrob-methods.Rd man/getMeta-methods.Rd man/ideoView.Rd man/lohSpec.Rd man/MutationAnnotationFormat_v2.2-class.Rd man/cytoGeno.Rd
inst/CITATION
inst/extdata/brca.maf
inst/extdata/FLX0050Naive.vep
inst/extdata/FL.gms
inst/extdata/FLX001-Naive.gms_test
inst/extdata/FLX0010Naive.vep
inst/extdata/FLX0070Naive.vep
inst/extdata/FLX0040Naive.vep
inst/extdata/FLX0030Naive.vep
inst/extdata/FLX003-Naive.gms_test
inst/doc/Intro.html
inst/doc/waterfall_introduction.R inst/doc/Intro.Rmd inst/doc/Upcoming_Features.R
inst/doc/waterfall_introduction.html
inst/doc/Upcoming_Features.Rmd
inst/doc/Upcoming_Features.html
inst/doc/waterfall_introduction.Rmd inst/doc/Intro.R
data/brcaMAF.rda
data/LucCNseg.rda
data/cytoGeno.rda
data/SNPloci.rda
data/HCC1395_T.rda
data/PIK3CA.rda
data/HCC1395_Germline.rda
data/HCC1395_N.rda
data/hg19chr.rda
assets/Small_Variants_OO.ai
assets/Small_Variants_OO.png
build/vignette.rds
vignettes/Intro.Rmd vignettes/Upcoming_Features.Rmd vignettes/waterfall_introduction.Rmd
GenVisR documentation built on Dec. 28, 2020, 2 a.m.

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