diffloop

This package is for version 3.7 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: 3.7

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>

Citation (from within R, enter citation("diffloop")):

Installation

To install this package, start R (version "3.5") 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")
diffloop: Identifying differential DNA loops from chromatin topology data. HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, DataRepresentation, GO, Preprocessing, QualityControl, Software, Visualization
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License MIT + file LICENSE
Depends
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
System Requirements
URL https://github.com/aryeelab/diffloop
Bug Reports https://github.com/aryeelab/diffloop/issues
See More
Suggests DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat
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 diffloop_1.8.0.tar.gz
Windows Binary diffloop_1.8.0.zip
Mac OS X 10.11 (El Capitan) diffloop_1.8.0.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
Old Source Packages for BioC 3.7 Source Archive