To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("REDseq")
In most cases, you don't need to download the package archive at all.
REDseq
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Bioconductor version: 2.14
The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.
Author: Lihua Julie Zhu and Thomas Fazzio
Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>
Citation (from within R,
enter citation("REDseq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("REDseq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("REDseq")
| R Script | REDseq Vignette | |
| Reference Manual |
Details
| biocViews | Preprocessing, SequenceMatching, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL (>=2) |
| Depends | R (>= 2.15.0), BiocGenerics(>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno |
| Imports | BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges(>= 1.13.5), multtest, stats, utils |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | REDseq_1.10.0.tar.gz |
| Windows Binary | REDseq_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | REDseq_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | REDseq_1.10.0.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
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2014
