To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("REDseq")
In most cases, you don't need to download the package archive at all.
REDseq
|
This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see REDseq.
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Bioconductor version: 3.1
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:
## try http:// if https:// URLs are not supported
source("https://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 | 1.14.1 |
| In Bioconductor since | BioC 2.9 (R-2.14) (4.5 years) |
| 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 |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | REDseq_1.14.1.tar.gz |
| Windows Binary | REDseq_1.14.1.zip |
| Mac OS X 10.6 (Snow Leopard) | REDseq_1.14.1.tgz |
| Mac OS X 10.9 (Mavericks) | REDseq_1.14.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/REDseq/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/REDseq/ |
| Package Downloads Report | Download Stats |
Documentation »
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