To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("r3Cseq")
In most cases, you don't need to download the package archive at all.
r3Cseq
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Bioconductor version: 3.0
This package is an implementation of data analysis for the long-range interactions from 3C-seq assay.
Author: Supat Thongjuea, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK <supat.thongjuea at ndcls.ox.ac.uk>
Maintainer: Supat Thongjuea <supat.thongjuea at ndcls.ox.ac.uk>
Citation (from within R,
enter citation("r3Cseq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("r3Cseq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("r3Cseq")
| R Script | r3Cseq | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Preprocessing, Sequencing, Software |
| Version | 1.12.1 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL-3 |
| Depends | GenomicRanges, Rsamtools, data.table, rtracklayer, VGAM, qvalue, RColorBrewer, sqldf, methods |
| Imports | |
| LinkingTo | |
| Suggests | BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked |
| SystemRequirements | |
| Enhances | |
| URL | http://r3cseq.genereg.net |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | r3Cseq_1.12.1.tar.gz |
| Windows Binary | r3Cseq_1.12.1.zip |
| Mac OS X 10.6 (Snow Leopard) | r3Cseq_1.12.1.tgz |
| Mac OS X 10.9 (Mavericks) | r3Cseq_1.12.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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