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 (3.15)

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 <krismer at mit.edu>, David Gifford <gifford at mit.edu>

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 (!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

PDF   Reference Manual

Details

biocViews Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software
Version 1.9.0
In Bioconductor since BioC 3.10 (R-3.6) (2 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, 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
Windows Binary
macOS 10.13 (High Sierra)
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/
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