hicVennDiagram
This is the released version of hicVennDiagram; for the devel version, see hicVennDiagram.
Venn Diagram for genomic interaction data
Bioconductor version: Release (3.23)
A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.
Author: Jianhong Ou [aut, cre]
Maintainer: Jianhong Ou <jou at morgridge.org>
citation("hicVennDiagram")):
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")
BiocManager::install("hicVennDiagram")
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("hicVennDiagram")| hicVennDiagram Vignette: overview | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNA3DStructure, HiC, Software, Visualization |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0) |
| Imports | Seqinfo, GenomicRanges, IRanges, InteractionSet, rtracklayer, ggplot2, ComplexUpset, reshape2, eulerr, S4Vectors, methods, utils, htmlwidgets, svglite |
| System Requirements | |
| URL | https://github.com/jianhong/hicVennDiagram |
| Bug Reports | https://github.com/jianhong/hicVennDiagram/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid, TxDb.Hsapiens.UCSC.hg38.knownGene |
| 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 | hicVennDiagram_1.10.0.tar.gz |
| Windows Binary (x86_64) | hicVennDiagram_1.10.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | hicVennDiagram_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | hicVennDiagram_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/hicVennDiagram |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hicVennDiagram |
| Bioc Package Browser | https://code.bioconductor.org/browse/hicVennDiagram/ |
| Package Short Url | https://bioconductor.org/packages/hicVennDiagram/ |
| Package Downloads Report | Download Stats |