DOI: 10.18129/B9.bioc.idr2d  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see idr2d.

Irreproducible Discovery Rate for Genomic Interactions Data

Bioconductor version: 3.16

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>

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HTML R Script Identify reproducible genomic interactions from replicate ChIA-PET experiments
HTML R Script Identify reproducible genomic peaks from replicate ChIP-seq experiments
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biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software
Version 1.12.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 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
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
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