REDseq
This package is for version 3.7 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: 3.7
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("REDseq")
):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("REDseq")
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("REDseq")
REDseq Vignette | R Script | |
Reference Manual |
Details
biocViews | Preprocessing, SequenceMatching, Sequencing, Software |
Version | 1.26.0 |
In Bioconductor since | BioC 2.9 (R-2.14) (12.5 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 |
System Requirements | |
URL |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | REDseq_1.26.0.tar.gz |
Windows Binary | REDseq_1.26.0.zip |
Mac OS X 10.11 (El Capitan) | REDseq_1.26.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/REDseq |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/REDseq |
Package Short Url | https://bioconductor.org/packages/REDseq/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.7 | Source Archive |