idr2d
This is the released version of idr2d; for the devel version, see idr2d.
Irreproducible Discovery Rate for Genomic Interactions Data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | idr2d_1.26.0.tar.gz |
| Windows Binary (x86_64) | idr2d_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | idr2d_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | idr2d_1.26.0.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 |