GenomicInteractions
Utilities for handling genomic interaction data
Bioconductor version: Release (3.20)
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 | 1.40.0 |
| 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_1.40.0.tar.gz |
| Windows Binary (x86_64) | GenomicInteractions_1.40.0.zip |
| macOS Binary (x86_64) | GenomicInteractions_1.40.0.tgz |
| macOS Binary (arm64) | GenomicInteractions_1.40.0.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 |