Preliminaries: the data | Using epivizr | The epivizr app | Listing available chart types | Adding charts | Adding block region tracks | Modifying chart settings and colors | Printing charts | Adding line plots along the genome | Managing the app | Charts that are not aligned to genomic location | Adding a scatterplot | The RangedSummarizedExperiment Object | Visualizing data available from epiviz webserver | Load remote measurements | Query measurements and add charts | More application interactions | Slideshow | Printing the epivizr workspace | Saving the epivizr workspace | Restarting the epivizr workspace | Closing the session | Standalone version and browsing arbitrary genomes | SessionInfo
Package: epivizr 2.43.0
Hector Corrada Bravo
epivizr: R Interface to epiviz web app
This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.
Authors:
epivizr_2.43.0.tar.gz
epivizr_2.43.0.zip(r-4.7)epivizr_2.43.0.zip(r-4.6)epivizr_2.43.0.zip(r-4.5)
epivizr_2.43.0.tgz(r-4.6-any)epivizr_2.43.0.tgz(r-4.5-any)
epivizr_2.43.0.tar.gz(r-4.7-any)epivizr_2.43.0.tar.gz(r-4.6-any)
epivizr_2.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epivizr/json (API)
| # Install 'epivizr' in R: |
| install.packages('epivizr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- tcga_colon_blocks - Example methylation data (blocks) for epivizr vignette.
- tcga_colon_curves - Example methylation data (smoothed methylation levels) for epivizr vignette
- tcga_colon_expression - Example exon-level RNAseq data from TCGA project for epivizr vignette.
On BioConductor:epivizr-2.43.0(bioc 3.24)epivizr-2.42.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationinfrastructuregui
Last updated from:b2130b0780. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 368 | ||
| linux-devel-x86_64 | NOTE | 524 | ||
| source / vignettes | OK | 396 | ||
| linux-release-x86_64 | NOTE | 573 | ||
| macos-release-arm64 | NOTE | 254 | ||
| macos-oldrel-arm64 | NOTE | 337 | ||
| windows-devel | NOTE | 379 | ||
| windows-release | NOTE | 364 | ||
| windows-oldrel | NOTE | 348 | ||
| wasm-release | OK | 329 |
Exports:restartEpivizshowstartEpiviz
Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydigestdoRNGensembldbepivizrDataepivizrServerfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhttpuvhttrIRangesiteratorsjsonliteKEGGRESTlambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslOrganismDbiotelpkgconfigpngpromisesProtGenericsR6RBGLRcppRCurlrestfulrRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystatmodSummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class managing connection to epiviz application. | EpivizApp EpivizApp-class |
| Class encapsulating a chart in epiviz app | EpivizChart EpivizChart-class |
| Class providing chart manager for epiviz app | EpivizChartMgr EpivizChartMgr-class |
| Restart epiviz app connection and workspace. | restartEpiviz |
| Print information about EpivizChart | show,EpivizChart-method |
| Start epiviz app and create 'EpivizApp' object to manage connection. | startEpiviz |
| Example methylation data (blocks) for epivizr vignette. | tcga_colon_blocks |
| Example methylation data (smoothed methylation levels) for epivizr vignette | tcga_colon_curves |
| Example exon-level RNAseq data from TCGA project for epivizr vignette. | tcga_colon_expression |
