REDseq
This package is for version 3.9 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: 3.9
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 "3.6") 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 | 1.30.0 |
| 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 |
See More
| Suggests | |
| 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 | REDseq_1.30.0.tar.gz |
| Windows Binary | REDseq_1.30.0.zip |
| Mac OS X 10.11 (El Capitan) | REDseq_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/REDseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/REDseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/REDseq/ |
| Package Short Url | https://bioconductor.org/packages/REDseq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |