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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 (3.20)

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>

Maintainer: Supat Thongjuea <supat.thongjuea at> or <supat.thongjuea at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

r3Cseq PDF R Script
Reference Manual PDF


biocViews Preprocessing, Sequencing, Software
Version 1.51.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL-3
Depends GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
Imports methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer
System Requirements
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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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Follow Installation instructions to use this package in your R session.

Source Package r3Cseq_1.51.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) r3Cseq_1.51.0.tgz
macOS Binary (arm64) r3Cseq_1.51.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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