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

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Documentation for package ‘REDseq’ version 1.55.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

REDseq-package	REDseq
assignSeq2REsite	Assign mapped sequence tags to corresponding restriction enzyme (RE) cut sites
binom.test.REDseq	Binomial test for REDseq dataset
buildREmap	Build a genome wide cut site map for a Restriction Enzyme (RE)
compareREDseq	Compare two RED Sequencing Dataset
distanceHistSeq2RE	Plot the distance distribution from sequence to the associated RE sites
example.assignedREDseq	an example assigned REDseq dataset
example.map	an example REmap dataset
example.REDseq	an example sequencing dataset from a restoration enzyme digestion (RED) experiment
plotCutDistribution	plot cut frequencies of RE sites along a given chromosome
REDseq	REDseq
summarizeByRE	Output count/weight summary by restriction enzyme cut site ID (REid)
summarizeBySeq	Output count/weight summary by sequences