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 mit.edu>

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

Installation

To install this package, start R (version "4.2") and enter:


if (!require("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")
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
NEWS Text
LICENSE Text

Details

biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software
Version 1.12.0
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_1.12.0.tar.gz
Windows Binary idr2d_1.12.0.zip
macOS Binary (x86_64) idr2d_1.12.0.tgz
macOS Binary (arm64) idr2d_1.12.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.16 Source Archive