geomeTriD

This is the development version of geomeTriD; for the stable release version, see geomeTriD.

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

Bioconductor version: Development (3.21)

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] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software, Visualization
Version	1.1.1
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

Suggests	RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	geomeTriD_1.1.1.tar.gz
Windows Binary (x86_64)	geomeTriD_1.1.1.zip
macOS Binary (x86_64)	geomeTriD_1.1.1.tgz
macOS Binary (arm64)
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