Package: GenVisR 1.37.0
Zachary Skidmore
GenVisR: Genomic Visualizations in R
Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.
Authors:
GenVisR_1.37.0.tar.gz
GenVisR_1.37.0.zip(r-4.5)GenVisR_1.37.0.zip(r-4.4)GenVisR_1.37.0.zip(r-4.3)
GenVisR_1.37.0.tgz(r-4.4-any)GenVisR_1.37.0.tgz(r-4.3-any)
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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')) |
Bug tracker:https://github.com/griffithlab/genvisr/issues
On BioConductor:GenVisR-1.37.0(bioc 3.20)GenVisR-1.36.0(bioc 3.19)
Last updated 2 months agofrom:3b6df4fc29
Exports:ClinicalcnFreqcnSpeccnViewcompIdentcovBarsdrawPlotgenCovgeneVizgetDatagetDescriptiongetGrobgetHeadergetMetagetMutationgetPathgetPositiongetSamplegetVersionGMSideoViewlohSpeclohViewlolliplotLolliplotMutationAnnotationFormatMutSpectraRainfallTvTiVEPwaterfallWaterfallwriteData
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablegtoolshmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Truncated BRCA MAF file | brcaMAF |
| Class Clinical | Clinical Clinical-class |
| Construct copy-number frequency plot | cnFreq |
| Construct copy-number cohort plot | cnSpec |
| Construct copy-number single sample plot | cnView |
| Construct identity snp comparison plot | compIdent |
| Construct an overall coverage cohort plot | covBars |
| Cytogenetic banding dataset | cytoGeno |
| Method drawPlot | drawPlot drawPlot,Clinical-method drawPlot,Lolliplot-method drawPlot,MutSpectra-method drawPlot,Rainfall-method drawPlot,Waterfall-method |
| Construct a region of interest coverage plot | genCov |
| Construct a gene-features plot | geneViz |
| GenVisR | GenVisR |
| 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 getDescription | getDescription getDescription,VEP-method getDescription,VEP_Virtual-method |
| Method getGrob | getGrob 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 getHeader | getHeader getHeader,VEP-method getHeader,VEP_Virtual-method |
| Method getMeta | getMeta getMeta,GMS-method getMeta,GMS_Virtual-method getMeta,MutationAnnotationFormat-method getMeta,MutationAnnotationFormat_Virtual-method getMeta,VEP-method getMeta,VEP_Virtual-method |
| Method getMutation | getMutation getMutation,GMS-method getMutation,GMS_Virtual-method getMutation,MutationAnnotationFormat-method getMutation,MutationAnnotationFormat_Virtual-method getMutation,VEP-method getMutation,VEP_Virtual-method |
| Method getPath | getPath getPath,GMS-method getPath,MutationAnnotationFormat-method getPath,VEP-method |
| Method getPosition | getPosition getPosition,GMS-method getPosition,GMS_Virtual-method getPosition,MutationAnnotationFormat-method getPosition,MutationAnnotationFormat_Virtual-method getPosition,VEP-method getPosition,VEP_Virtual-method |
| Method getSample | getSample getSample,GMS-method getSample,GMS_Virtual-method getSample,MutationAnnotationFormat-method getSample,MutationAnnotationFormat_Virtual-method getSample,VEP-method getSample,VEP_Virtual-method |
| Method getVersion | getVersion getVersion,GMS-method getVersion,MutationAnnotationFormat-method getVersion,VEP-method |
| Class GMS_v4 | GMS_v4 GMS_v4-class |
| Class GMS_Virtual | GMS_Virtual-class |
| Class GMS | GMS GMS-class |
| Germline Calls | HCC1395_Germline |
| Normal BAM | HCC1395_N |
| Tumor BAM | HCC1395_T |
| hg19 chromosome boundaries | hg19chr |
| Construct an ideogram | ideoView |
| Plot LOH data | lohSpec |
| Construct LOH chromosome plot | lohView |
| Construct a lolliplot | lolliplot |
| Class Lolliplot | Lolliplot Lolliplot-class |
| Truncated CN segments | LucCNseg |
| Class MutationAnnotationFormat_v1.0 | MutationAnnotationFormat_v1.0 MutationAnnotationFormat_v1.0-class |
| Class MutationAnnotationFormat_v2.0 | MutationAnnotationFormat_v2.0 MutationAnnotationFormat_v2.0-class |
| Class MutationAnnotationFormat_v2.1 | MutationAnnotationFormat_v2.1 MutationAnnotationFormat_v2.1-class |
| Class MutationAnnotationFormat_v2.2 | MutationAnnotationFormat_v2.2 MutationAnnotationFormat_v2.2-class |
| Class MutationAnnotationFormat_v2.3 | MutationAnnotationFormat_v2.3 MutationAnnotationFormat_v2.3-class |
| Class MutationAnnotationFormat_v2.4 | MutationAnnotationFormat_v2.4 MutationAnnotationFormat_v2.4-class |
| Class MutationAnnotationFormat_Virtual | MutationAnnotationFormat_Virtual-class |
| Class MutationAnnotationFormat | MutationAnnotationFormat MutationAnnotationFormat-class |
| Class MutSpectra | MutSpectra MutSpectra-class |
| Subset MAF file for PIK3CA gene | PIK3CA |
| Class Rainfall | Rainfall Rainfall-class |
| Identity snps | SNPloci |
| Construct transition-transversion plot | TvTi |
| Class VEP_v88 | VEP_v88 VEP_v88-class |
| Class VEP_Virtual | VEP_Virtual-class |
| Class VEP | VEP VEP-class |
| Construct a oncoprint | waterfall |
| Class Waterfall | Waterfall Waterfall-class |
| Method writeData | writeData 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 |
