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 (3.24)
The geomeTriD (Three-Dimensional Geometry) Package provides interactive 3D visualization of chromatin structures using the WebGL-based 'three.js' (https://threejs.org/) or the rgl rendering library. It is designed to identify and explore spatial chromatin patterns within genomic regions. The package generates dynamic 3D plots and HTML widgets that integrate seamlessly with Shiny applications, enabling researchers to visualize chromatin organization, detect spatial features, and compare structural dynamics across different conditions and data types.
Author: Jianhong Ou [aut, cre]
, Kenneth Poss [aut, fnd]
Maintainer: Jianhong Ou <jou at morgridge.org>
citation("geomeTriD")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Software, Visualization |
| Version | 1.7.1 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | aricode, BiocGenerics, Biostrings, clue, cluster, dbscan, future.apply, Seqinfo, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, progressr, RANN, 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, BSgenome.Hsapiens.UCSC.hg19, 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_1.7.1.tar.gz |
| Windows Binary (x86_64) | geomeTriD_1.7.1.zip |
| macOS Binary (big-sur-x86_64) | geomeTriD_1.7.1.tgz |
| macOS Binary (sonoma-arm64) | geomeTriD_1.7.1.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 |