r3Cseq
This is the development version of r3Cseq; for the stable release version, see r3Cseq.
All Bioconductor versions of r3Cseq
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Bioconductor version: 3.24 · Package version: 1.59.0
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"):
Supat Thongjuea, MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, UK. r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq). doi:10.18129/B9.bioc.r3Cseq, R package version 1.59.0, https://bioconductor.org/packages/r3Cseq.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("r3Cseq")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.59.0 |
| License | GPL-3 |
| URL | http://r3cseq.genereg.net https://github.com/supatt-lab/r3Cseq/ |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.9 (R-2.14) (14 years) |
| Downloads rank | 462 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Preprocessing, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/r3Cseq/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("r3Cseq")| r3Cseq | R Script | |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | r3Cseq_1.59.0.tar.gz |
| Windows binary (x86_64) | r3Cseq_1.59.0.zip |
| macOS binary (arm64) | r3Cseq_1.59.0.tgz |
| macOS binary (x86_64) | r3Cseq_1.59.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/r3Cseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/r3Cseq |
| Package Downloads Report | Download Stats |
Dependencies
Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
Imports: methods, Seqinfo, IRanges, Biostrings, data.table, sqldf, RColorBrewer
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