geomeTriD

A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data


Bioconductor version: Release (3.20)

geomeTriD (Three Dimensional Geometry Package) create interactive 3D plots using the GL library with the 'three.js' visualization library (https://threejs.org) or the rgl library. In addition to creating interactive 3D plots, the application also generates simplified models in 2D. These 2D models provide a more straightforward visual representation, making it easier to analyze and interpret the data quickly. This functionality ensures that users have access to both detailed three-dimensional visualizations and more accessible two-dimensional views, catering to various analytical needs.

Author: Jianhong Ou [aut, cre]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Citation (from within R, enter citation("geomeTriD")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("geomeTriD")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("geomeTriD")
geomeTriD Vignette: Plot data in 3D HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.20 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports BiocGenerics, GenomeInfoDb, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, rgl, rjson, S4Vectors, scales, stats, trackViewer
System Requirements
URL https://github.com/jianhong/geomeTriD
Bug Reports https://github.com/jianhong/geomeTriD/issues
See More
Suggests RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat
Linking To
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Depends On Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package geomeTriD_1.0.0.tar.gz
Windows Binary (x86_64) geomeTriD_1.0.0.zip
macOS Binary (x86_64) geomeTriD_1.0.0.tgz
macOS Binary (arm64) geomeTriD_0.99.18.tgz
Source Repository git clone https://git.bioconductor.org/packages/geomeTriD
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/geomeTriD
Bioc Package Browser https://code.bioconductor.org/browse/geomeTriD/
Package Short Url https://bioconductor.org/packages/geomeTriD/
Package Downloads Report Download Stats