idr2d

DOI: 10.18129/B9.bioc.idr2d    

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

Irreproducible Discovery Rate for Genomic Interactions Data

Bioconductor version: Development (3.11)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.1
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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 (>= 2.0.1)
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_1.1.1.tar.gz
Windows Binary idr2d_1.1.1.zip
Mac OS X 10.11 (El Capitan) idr2d_1.1.1.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

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