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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/REDseq.html below:

Bioconductor - REDseq (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews Preprocessing, SequenceMatching, Sequencing, Software Version 1.55.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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 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.

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