GenomicInteractions
Utilities for handling genomic interaction data
Bioconductor version: Release (3.19)
Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.
Author: Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B.
Maintainer: Liz Ing-Simmons <liz.ingsimmons at gmail.com>
Citation (from within R, enter
citation("GenomicInteractions")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicInteractions")
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("GenomicInteractions")
chiapet_vignette.html | HTML | R Script |
GenomicInteractions-HiC | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DataImport, DataRepresentation, HiC, Infrastructure, Software |
Version | 1.38.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (10 years) |
License | GPL-3 |
Depends | R (>= 3.5), InteractionSet |
Imports | Rsamtools, rtracklayer, GenomicRanges(>= 1.29.6), IRanges, BiocGenerics(>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors(>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices |
System Requirements | |
URL | https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/ |
See More
Suggests | knitr, rmarkdown, BiocStyle, testthat |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | CAGEfightR, extraChIPs, spatzie, OHCA |
Suggests Me | Chicago, ELMER, sevenC, chicane |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | GenomicInteractions_1.38.0.tar.gz |
Windows Binary | GenomicInteractions_1.38.0.zip (64-bit only) |
macOS Binary (x86_64) | GenomicInteractions_1.38.0.tgz |
macOS Binary (arm64) | GenomicInteractions_1.38.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/GenomicInteractions |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicInteractions |
Bioc Package Browser | https://code.bioconductor.org/browse/GenomicInteractions/ |
Package Short Url | https://bioconductor.org/packages/GenomicInteractions/ |
Package Downloads Report | Download Stats |