DOI: 10.18129/B9.bioc.GenomicInteractions  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GenomicInteractions.

Utilities for handling genomic interaction data

Bioconductor version: 3.16

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>

Citation (from within R, enter citation("GenomicInteractions")):


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HTML R Script chiapet_vignette.html
HTML R Script GenomicInteractions-HiC
PDF   Reference Manual
Text   NEWS


biocViews DataImport, DataRepresentation, HiC, Infrastructure, Software
Version 1.32.0
In Bioconductor since BioC 3.0 (R-3.1) (8.5 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
Suggests knitr, rmarkdown, BiocStyle, testthat
Depends On Me
Imports Me CAGEfightR, extraChIPs, HiCDCPlus, HiContacts, spatzie
Suggests Me Chicago, ELMER, sevenC
Links To Me
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