Package: epivizr 2.37.0
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_2.37.0.tar.gz
epivizr_2.37.0.zip(r-4.5)epivizr_2.37.0.zip(r-4.4)epivizr_2.37.0.zip(r-4.3)
epivizr_2.37.0.tgz(r-4.4-any)epivizr_2.37.0.tgz(r-4.3-any)
epivizr_2.37.0.tar.gz(r-4.5-noble)epivizr_2.37.0.tar.gz(r-4.4-noble)
epivizr_2.37.0.tgz(r-4.4-emscripten)epivizr_2.37.0.tgz(r-4.3-emscripten)
epivizr.pdf |epivizr.html✨
epivizr/json (API)
NEWS
| # Install 'epivizr' in R: |
| install.packages('epivizr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- 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-2.37.0(bioc 3.21)epivizr-2.36.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
visualizationinfrastructuregui
Last updated 2 months agofrom:4241f769d9. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 17 2024 |
| R-4.5-win | NOTE | Dec 17 2024 |
| R-4.5-linux | NOTE | Dec 17 2024 |
| R-4.4-win | NOTE | Dec 17 2024 |
| R-4.4-mac | NOTE | Dec 17 2024 |
| R-4.3-win | NOTE | Dec 17 2024 |
| R-4.3-mac | NOTE | Dec 17 2024 |
Exports:restartEpivizshowstartEpiviz
Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbumphuntercachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdoRNGdplyrensembldbepivizrDataepivizrServerfansifastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhmshttpuvhttrhttr2IRangesiteratorsjsonliteKEGGRESTlambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslOrganismDbipillarpkgconfigplogrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRBGLRcppRCurlrestfulrRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc
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 |
