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 (3.23)
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")):
Installation
To install this package, start R (version "4.6") 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
| Reference Manual |
Details
| biocViews | Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 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) |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |