diffloop

DOI: 10.18129/B9.bioc.diffloop    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see diffloop.

Identifying differential DNA loops from chromatin topology data

Bioconductor version: 3.15

A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.

Author: Caleb Lareau [aut, cre], Martin Aryee [aut]

Maintainer: Caleb Lareau <caleblareau at g.harvard.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("diffloop")

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("diffloop")

 

HTML	R Script	diffloop: Identifying differential DNA loops from chromatin topology data.
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, GO, Preprocessing, QualityControl, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0)
Imports	methods, GenomicRanges, foreach, plyr, dplyr, reshape2, ggplot2, matrixStats, Sushi, edgeR, locfit, statmod, biomaRt, GenomeInfoDb, S4Vectors, IRanges, grDevices, graphics, stats, utils, Biobase, readr, data.table, rtracklayer, pbapply, limma
LinkingTo
Suggests	DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/aryeelab/diffloop
BugReports	https://github.com/aryeelab/diffloop/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	diffloop_1.24.0.tar.gz
Windows Binary	diffloop_1.24.0.zip
macOS Binary (x86_64)	diffloop_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/diffloop
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/diffloop
Package Short Url	https://bioconductor.org/packages/diffloop/
Package Downloads Report	Download Stats