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Bioconductor - idr2d (development version)

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 (3.22)

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] ORCID: 0000-0001-8994-3416 , David Gifford [ths, cph] ORCID: 0000-0003-1709-4034

Maintainer: Konstantin Krismer <krismer at mit.edu>

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

To install this package, start R (version "4.5") and enter:


if (!require("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")
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 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 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 Package Archives

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

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