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REDseq

This is the development version of REDseq; for the stable release version, see REDseq.

Analysis of high-throughput sequencing data processed by restriction enzyme digestion


Bioconductor version: Development (3.19)

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, Junhui Li 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 (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF R Script
Reference Manual PDF

Details

biocViews Preprocessing, SequenceMatching, Sequencing, Software
Version 1.49.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL (>=2)
Depends R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno
Imports AnnotationDbi, graphics, IRanges(>= 1.13.5), stats, utils
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package REDseq_1.49.0.tar.gz
Windows Binary
macOS Binary (x86_64) REDseq_1.49.0.tgz
macOS Binary (arm64)
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