r3Cseq
This package is for version 3.11 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: 3.11
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("r3Cseq")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Preprocessing, Sequencing, Software |
| Version | 1.34.0 |
| 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 | |
| URL | http://r3cseq.genereg.net https://github.com/supatt-lab/r3Cseq/ |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | r3Cseq_1.34.0.tar.gz |
| Windows Binary | r3Cseq_1.34.0.zip |
| macOS 10.13 (High Sierra) | r3Cseq_1.34.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |