idr2d
Irreproducible Discovery Rate for Genomic Interactions Data
Bioconductor version: 3.23 · Package version: 1.26.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("idr2d")Details
| Maintainer | Konstantin Krismer <krismer@mit.edu> |
| Author | Konstantin Krismer [aut, cre, cph] (ORCID: <https://orcid.org/0000-0001-8994-3416>), David Gifford [ths, cph] (ORCID: <https://orcid.org/0000-0003-1709-4034>) |
| License | MIT + file LICENSE |
| URL | https://idr2d.mit.edu |
| System Requirements | Python (>= 3.5.0), hic-straw |
| Downloads rank | 313 |
| Source branch | RELEASE_3_23 |
| biocViews | Classification, DNA3DStructure, Epigenetics, FunctionalGenomics, GeneRegulation, HiC, PeakDetection, Software |
Documentation
- Identify reproducible genomic interactions from replicate ChIA-PET experiments
- Identify reproducible genomic peaks from replicate ChIP-seq experiments
Download
Dependencies
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
Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0)