GenomicInteractions

This is the released version of GenomicInteractions; for the devel version, see GenomicInteractions.

Utilities for handling genomic interaction data

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.GenomicInteractions

Bioconductor version: Release (3.22)

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 "4.5") 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, HiC, Infrastructure, Software

Version 1.44.0

In Bioconductor since BioC 3.0 (R-3.1) (11 years)

License GPL-3

Depends R (>= 3.5), InteractionSet

Imports Rsamtools, rtracklayer, GenomicRanges(>= 1.29.6), IRanges, BiocGenerics(>= 0.15.3), data.table, stringr, Seqinfo, ggplot2, grid, gridExtra, methods, igraph, S4Vectors(>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices

System Requirements

URL https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/

Suggests knitr, rmarkdown, BiocStyle, testthat

Linking To

Enhances

Depends On Me

Imports Me CAGEfightR, HiCaptuRe, OHCA

Suggests Me Chicago, ELMER, extraChIPs, linkSet, 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_1.44.0.tar.gz

Windows Binary (x86_64) GenomicInteractions_1.43.1.zip

macOS Binary (x86_64) GenomicInteractions_1.44.0.tgz

macOS Binary (arm64) GenomicInteractions_1.44.0.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