Package: GenVisR 1.39.0

Zachary Skidmore

GenVisR: Genomic Visualizations in R

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

Authors:Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut], Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith [aut]

GenVisR_1.39.0.tar.gz
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GenVisR.pdf |GenVisR.html✨
GenVisR/json (API)
NEWS

# Install 'GenVisR' in R:
install.packages('GenVisR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/griffithlab/genvisr/issues

Datasets:

On BioConductor:GenVisR-1.39.0(bioc 3.21)GenVisR-1.38.0(bioc 3.20)

infrastructuredatarepresentationclassificationdnaseq

9.85 score 212 stars 79 scripts 511 downloads 54 mentions 33 exports 114 dependencies

Last updated 2 months agofrom:cf208dcea1. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winNOTEDec 19 2024
R-4.3-macNOTEDec 19 2024

Exports:ClinicalcnFreqcnSpeccnViewcompIdentcovBarsdrawPlotgenCovgeneVizgetDatagetDescriptiongetGrobgetHeadergetMetagetMutationgetPathgetPositiongetSamplegetVersionGMSideoViewlohSpeclohViewlolliplotLolliplotMutationAnnotationFormatMutSpectraRainfallTvTiVEPwaterfallWaterfallwriteData

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablegtoolshmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrXMLxml2XVectoryamlzlibbioc

GenVisR: An introduction

Zachary Skidmore

Rendered fromIntro.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2022-09-04
Started: 2018-04-27

waterfall: function introduction

Zachary Skidmore

Rendered fromwaterfall_introduction.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-04-27
Started: 2016-03-11

Readme and manuals

Help Manual

Help pageTopics
Truncated BRCA MAF filebrcaMAF
Class ClinicalClinical Clinical-class
Construct copy-number frequency plotcnFreq
Construct copy-number cohort plotcnSpec
Construct copy-number single sample plotcnView
Construct identity snp comparison plotcompIdent
Construct an overall coverage cohort plotcovBars
Cytogenetic banding datasetcytoGeno
Method drawPlotdrawPlot drawPlot,Clinical-method drawPlot,Lolliplot-method drawPlot,MutSpectra-method drawPlot,Rainfall-method drawPlot,Waterfall-method
Construct a region of interest coverage plotgenCov
Construct a gene-features plotgeneViz
GenVisRGenVisR
Method getData.getData_Lolliplot .getData_MutSpectra .getData_Rainfall .getData_waterfall getData getData,Clinical-method getData,ClinicalData-method getData,Lolliplot-method getData,LolliplotData-method getData,MutSpectra-method getData,MutSpectraPrimaryData-method getData,Rainfall-method getData,RainfallPrimaryData-method getData,Waterfall-method getData,WaterfallData-method
Method getDescriptiongetDescription getDescription,VEP-method getDescription,VEP_Virtual-method
Method getGrobgetGrob getGrob,Lolliplot-method getGrob,LolliplotPlots-method getGrob,MutSpectra-method getGrob,MutSpectraPlots-method getGrob,Rainfall-method getGrob,RainfallPlots-method getGrob,Waterfall-method getGrob,WaterfallPlots-method
Method getHeadergetHeader getHeader,VEP-method getHeader,VEP_Virtual-method
Method getMetagetMeta getMeta,GMS-method getMeta,GMS_Virtual-method getMeta,MutationAnnotationFormat-method getMeta,MutationAnnotationFormat_Virtual-method getMeta,VEP-method getMeta,VEP_Virtual-method
Method getMutationgetMutation getMutation,GMS-method getMutation,GMS_Virtual-method getMutation,MutationAnnotationFormat-method getMutation,MutationAnnotationFormat_Virtual-method getMutation,VEP-method getMutation,VEP_Virtual-method
Method getPathgetPath getPath,GMS-method getPath,MutationAnnotationFormat-method getPath,VEP-method
Method getPositiongetPosition getPosition,GMS-method getPosition,GMS_Virtual-method getPosition,MutationAnnotationFormat-method getPosition,MutationAnnotationFormat_Virtual-method getPosition,VEP-method getPosition,VEP_Virtual-method
Method getSamplegetSample getSample,GMS-method getSample,GMS_Virtual-method getSample,MutationAnnotationFormat-method getSample,MutationAnnotationFormat_Virtual-method getSample,VEP-method getSample,VEP_Virtual-method
Method getVersiongetVersion getVersion,GMS-method getVersion,MutationAnnotationFormat-method getVersion,VEP-method
Class GMS_v4GMS_v4 GMS_v4-class
Class GMS_VirtualGMS_Virtual-class
Class GMSGMS GMS-class
Germline CallsHCC1395_Germline
Normal BAMHCC1395_N
Tumor BAMHCC1395_T
hg19 chromosome boundarieshg19chr
Construct an ideogramideoView
Plot LOH datalohSpec
Construct LOH chromosome plotlohView
Construct a lolliplotlolliplot
Class LolliplotLolliplot Lolliplot-class
Truncated CN segmentsLucCNseg
Class MutationAnnotationFormat_v1.0MutationAnnotationFormat_v1.0 MutationAnnotationFormat_v1.0-class
Class MutationAnnotationFormat_v2.0MutationAnnotationFormat_v2.0 MutationAnnotationFormat_v2.0-class
Class MutationAnnotationFormat_v2.1MutationAnnotationFormat_v2.1 MutationAnnotationFormat_v2.1-class
Class MutationAnnotationFormat_v2.2MutationAnnotationFormat_v2.2 MutationAnnotationFormat_v2.2-class
Class MutationAnnotationFormat_v2.3MutationAnnotationFormat_v2.3 MutationAnnotationFormat_v2.3-class
Class MutationAnnotationFormat_v2.4MutationAnnotationFormat_v2.4 MutationAnnotationFormat_v2.4-class
Class MutationAnnotationFormat_VirtualMutationAnnotationFormat_Virtual-class
Class MutationAnnotationFormatMutationAnnotationFormat MutationAnnotationFormat-class
Class MutSpectraMutSpectra MutSpectra-class
Subset MAF file for PIK3CA genePIK3CA
Class RainfallRainfall Rainfall-class
Identity snpsSNPloci
Construct transition-transversion plotTvTi
Class VEP_v88VEP_v88 VEP_v88-class
Class VEP_VirtualVEP_Virtual-class
Class VEPVEP VEP-class
Construct a oncoprintwaterfall
Class WaterfallWaterfall Waterfall-class
Method writeDatawriteData writeData,GMS-method writeData,GMS_Virtual writeData,GMS_Virtual-method writeData,MutationAnnotationFormat-method writeData,MutationAnnotationFormat_Virtual writeData,MutationAnnotationFormat_Virtual-method writeData,VEP-method writeData,VEP_Virtual writeData,VEP_Virtual-method