epivizr: R Interface to epiviz web app

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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.

Author
Hector Corrada Bravo, Florin Chelaru, Llewellyn Smith, Naomi Goldstein, Jayaram Kancherla, Morgan Walter
Date of publication
None
Maintainer
Hector Corrada Bravo <hcorrada@gmail.com>
License
Artistic-2.0
Version
2.4.0

View on Bioconductor

Man pages

EpivizApp-class
Class managing connection to epiviz application.
EpivizChart-class
Class encapsulating a chart in epiviz app
EpivizChartMgr-class
Class providing chart manager for epiviz app
show-EpivizChart-method
Print information about EpivizChart
startEpiviz
Start epiviz app and create 'EpivizApp' object to manage...
tcga_colon_blocks
Example methylation data (blocks) for epivizr vignette.
tcga_colon_curves
Example methylation data (smoothed methylation levels) for...
tcga_colon_expression
Example exon-level RNAseq data from TCGA project for epivizr...

Files in this package

epivizr/DESCRIPTION
epivizr/NAMESPACE
epivizr/R
epivizr/R/EpivizApp-class.R
epivizr/R/EpivizChart-class.R
epivizr/R/EpivizChartMgr-class.R
epivizr/R/settings_utils.R
epivizr/R/startEpiviz.R
epivizr/R/vignette_data.R
epivizr/README.md
epivizr/build
epivizr/build/vignette.rds
epivizr/data
epivizr/data/tcga_colon_blocks.rda
epivizr/data/tcga_colon_curves.rda
epivizr/data/tcga_colon_expression.rda
epivizr/inst
epivizr/inst/NEWS.Rd
epivizr/inst/doc
epivizr/inst/doc/IntroToEpivizr.R
epivizr/inst/doc/IntroToEpivizr.Rmd
epivizr/inst/doc/IntroToEpivizr.html
epivizr/man
epivizr/man/EpivizApp-class.Rd
epivizr/man/EpivizChart-class.Rd
epivizr/man/EpivizChartMgr-class.Rd
epivizr/man/show-EpivizChart-method.Rd
epivizr/man/startEpiviz.Rd
epivizr/man/tcga_colon_blocks.Rd
epivizr/man/tcga_colon_curves.Rd
epivizr/man/tcga_colon_expression.Rd
epivizr/tests
epivizr/tests/connected_tests
epivizr/tests/connected_tests/helper-makeEset.R
epivizr/tests/connected_tests/helper-organismdb.R
epivizr/tests/connected_tests/helper-phantomjs.R
epivizr/tests/connected_tests/helper-setOptions.R
epivizr/tests/connected_tests/helper-startmgr.R
epivizr/tests/connected_tests/helper-wait_until.R
epivizr/tests/connected_tests/index.html
epivizr/tests/connected_tests/test-add_charts.R
epivizr/tests/connected_tests/test-app_update.R
epivizr/tests/connected_tests/test-browsing.R
epivizr/tests/connected_tests/test-creation.R
epivizr/tests/connected_tests/test-manage_charts.R
epivizr/tests/connected_tests/test-plot_app.R
epivizr/tests/connected_tests/test-startEpiviz.R
epivizr/tests/testthat
epivizr/tests/testthat.R
epivizr/tests/testthat/helper-makeEset.R
epivizr/tests/testthat/helper-organismdb.R
epivizr/tests/testthat/helper-setOptions.R
epivizr/tests/testthat/helper-startmgr.R
epivizr/tests/testthat/helper-wait_until.R
epivizr/tests/testthat/test-add_charts.R
epivizr/tests/testthat/test-app_update.R
epivizr/tests/testthat/test-browsing.R
epivizr/tests/testthat/test-creation.R
epivizr/tests/testthat/test-manage_charts.R
epivizr/tests/testthat/test-plot_app.R
epivizr/tests/testthat/test-plot_methods.R
epivizr/tests/testthat/test-startEpiviz.R
epivizr/vignettes
epivizr/vignettes/IntroToEpivizr.Rmd