idr2d

DOI: 10.18129/B9.bioc.idr2d    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see idr2d.

Irreproducible Discovery Rate for Genomic Interactions Data

Bioconductor version: 3.11

A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks.

Author: Konstantin Krismer [aut, cre, cph] , David Gifford [ths, cph]

Maintainer: Konstantin Krismer <krismer at mit.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("idr2d")

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("idr2d")

 

HTML	R Script	Identify reproducible genomic interactions from replicate ChIA-PET experiments
HTML	R Script	Identify reproducible genomic peaks from replicate ChIP-seq experiments
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software
Version	1.2.2
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	MIT + file LICENSE
Depends	R (>= 3.6)
Imports	dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb(>= 1.14.0), GenomicRanges(>= 1.30), ggplot2 (>= 3.1.1), grDevices, idr (>= 1.2), IRanges(>= 2.18.0), magrittr (>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats, stringr (>= 1.3.1), utils
LinkingTo
Suggests	DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0)
SystemRequirements	Python (>= 3.5.0), hic-straw
Enhances
URL	https://idr2d.mit.edu
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	idr2d_1.2.2.tar.gz
Windows Binary	idr2d_1.2.2.zip
macOS 10.13 (High Sierra)	idr2d_1.2.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/idr2d
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/idr2d
Package Short Url	https://bioconductor.org/packages/idr2d/
Package Downloads Report	Download Stats