r3Cseq

DOI: 10.18129/B9.bioc.r3Cseq    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see r3Cseq.

Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

Bioconductor version: 3.15

This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.

Author: Supat Thongjuea, MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, UK <supat.thongjuea at imm.ox.ac.uk>

Maintainer: Supat Thongjuea <supat.thongjuea at imm.ox.ac.uk> or <supat.thongjuea at gmail.com>

Installation

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

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

BiocManager::install("r3Cseq")

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("r3Cseq")

 

PDF	R Script	r3Cseq
PDF		Reference Manual
Text		NEWS

Details

biocViews	Preprocessing, Sequencing, Software
Version	1.42.0
In Bioconductor since	BioC 2.9 (R-2.14) (11 years)
License	GPL-3
Depends	GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
Imports	methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer
LinkingTo
Suggests	BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked
SystemRequirements
Enhances
URL	http://r3cseq.genereg.net https://github.com/supatt-lab/r3Cseq/
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	r3Cseq_1.42.0.tar.gz
Windows Binary	r3Cseq_1.42.0.zip
macOS Binary (x86_64)	r3Cseq_1.42.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/r3Cseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/r3Cseq
Package Short Url	https://bioconductor.org/packages/r3Cseq/
Package Downloads Report	Download Stats