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This is the development version of idr2d; for the stable release version, see idr2d.

Irreproducible Discovery Rate for Genomic Interactions Data

Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("idr2d")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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:

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


biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
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, grid, idr (>= 1.2), IRanges(>= 2.18.0), magrittr (>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats, stringr (>= 1.3.1), utils
System Requirements Python (>= 3.5.0), hic-straw
URL https://idr2d.mit.edu
See More
Suggests DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0)
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Package Archives

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

Source Package idr2d_1.17.0.tar.gz
Windows Binary idr2d_1.17.0.zip
macOS Binary (x86_64) idr2d_1.17.0.tgz
macOS Binary (arm64) idr2d_1.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/idr2d
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/idr2d
Bioc Package Browser https://code.bioconductor.org/browse/idr2d/
Package Short Url https://bioconductor.org/packages/idr2d/
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