idr2d
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see idr2d.
Irreproducible Discovery Rate for Genomic Interactions Data
Bioconductor version: 3.13
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("idr2d")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software |
| Version | 1.6.0 |
| 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, 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | idr2d_1.6.0.tar.gz |
| Windows Binary | idr2d_1.6.0.zip |
| macOS 10.13 (High Sierra) | idr2d_1.6.0.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 3.13 | Source Archive |