r3Cseq

This package is for version 3.21 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: 3.21

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 "4.5") 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")

r3Cseq PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Preprocessing, Sequencing, Software

Version 1.54.0

In Bioconductor since BioC 2.9 (R-2.14) (14 years)

License GPL-3

Depends GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue

Imports methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer

System Requirements

URL http://r3cseq.genereg.net https://github.com/supatt-lab/r3Cseq/

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

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Package Archives

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

Source Package r3Cseq_1.54.0.tar.gz

Windows Binary (x86_64) r3Cseq_1.54.0.zip (64-bit only)

macOS Binary (x86_64) r3Cseq_1.54.0.tgz

macOS Binary (arm64) r3Cseq_1.54.0.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/

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