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r3Cseq

This is the development version of r3Cseq; for the stable release version, see r3Cseq.

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

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("r3Cseq")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
r3Cseq PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Preprocessing, Sequencing, Software
Version 1.47.0
In Bioconductor since BioC 2.9 (R-2.14) (12 years)
License GPL-3
Depends GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
Imports methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer
Linking To
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
System Requirements
Enhances
URL http://r3cseq.genereg.net https://github.com/supatt-lab/r3Cseq/
See More
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_1.47.0.tar.gz
Windows Binary r3Cseq_1.47.0.zip
macOS Binary (x86_64) r3Cseq_1.47.0.tgz
macOS Binary (arm64) r3Cseq_1.47.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/r3Cseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/r3Cseq
Bioc Package Browser https://code.bioconductor.org/browse/r3Cseq/
Package Short Url https://bioconductor.org/packages/r3Cseq/
Package Downloads Report Download Stats