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

Bioconductor version: Release (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>

Citation (from within R, enter citation("REDseq")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

REDseq Vignette PDF R Script
Reference Manual PDF


biocViews Preprocessing, SequenceMatching, Sequencing, Software
Version 1.50.0
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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Follow Installation instructions to use this package in your R session.

Source Package REDseq_1.50.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) REDseq_1.50.0.tgz
macOS Binary (arm64) REDseq_1.50.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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