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


[Up] [Top]

Documentation for package ‘REDseq’ version 1.20.0

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