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-package          REDseq
summarizeByRE           Output count/weight summary by restriction
                        enzyme cut site ID (REid)
summarizeBySeq          Output count/weight summary by sequences
