This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GenomicInteractions.
Bioconductor version: 3.9
R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / 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")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GenomicInteractions")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomicInteractions")
HTML | R Script | chiapet_vignette.html |
HTML | R Script | GenomicInteractions-HiC |
Reference Manual | ||
Text | NEWS |
biocViews | DataImport, DataRepresentation, HiC, Infrastructure, Software |
Version | 1.18.1 |
In Bioconductor since | BioC 3.0 (R-3.1) (5 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 |
LinkingTo | |
Suggests | knitr, BiocStyle, testthat |
SystemRequirements | |
Enhances | |
URL | https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/ |
Depends On Me | |
Imports Me | CAGEfightR |
Suggests Me | Chicago, ELMER, sevenC |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | GenomicInteractions_1.18.1.tar.gz |
Windows Binary | GenomicInteractions_1.18.1.zip |
Mac OS X 10.11 (El Capitan) | GenomicInteractions_1.18.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/GenomicInteractions |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicInteractions |
Package Short Url | https://bioconductor.org/packages/GenomicInteractions/ |
Package Downloads Report | Download Stats |
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