diffloop

DOI:10.18129/B9.bioc.diffloop

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seediffloop.

Identifying differential DNA loops from chromatin topology data

Bioconductor version: 3.14

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

Installation

To install this package, start R (version "4.1") and enter:

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

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.22.0
In Bioconductor since	BioC 3.3 (R-3.3) (6 years)
License	MIT + fileLICENSE
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
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

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	diffloop_1.22.0.tar.gz
Windows Binary	diffloop_1.22.0.zip
macOS 10.13 (High Sierra)	diffloop_1.22.0.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	//www.andersvercelli.com/packages/diffloop/
Package Downloads Report	Download Stats