GenomicInteractions
Utilities for handling genomic interaction data
Bioconductor version: 3.23 · Package version: 1.46.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicInteractions")Details
| Maintainer | Liz Ing-Simmons <liz.ingsimmons@gmail.com> |
| Author | Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard, B. |
| License | GPL-3 |
| URL | https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/ |
| Downloads rank | 1008 |
| Source branch | RELEASE_3_23 |
| biocViews | DataImport, DataRepresentation, HiC, Infrastructure, Software |
Documentation
- Package Vignette for Genomic Interactions: ChIA-PET data
- HiC vignette for GenomicInteractions package
Download
Follow the installation instructions to use this package in your R session.
| Source package | GenomicInteractions_1.46.0.tar.gz |
| Windows binary (x86_64) | GenomicInteractions_1.46.0.zip |
| macOS binary (arm64) | GenomicInteractions_1.46.0.tgz |
| macOS binary (x86_64) | GenomicInteractions_1.46.0.tgz |
Dependencies
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