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 and Thomas Fazzio|
|Date of publication||None|
|Maintainer||Lihua Julie Zhu <firstname.lastname@example.org>|
assignSeq2REsite: Assign mapped sequence tags to corresponding restriction...
binom.test.REDseq: Binomial test for REDseq dataset
buildREmap: Build a genome wide cut site map for a Restriction Enzyme...
compareREDseq: Compare two RED Sequencing Dataset
distanceHistSeq2RE: Plot the distance distribution from sequence to the...
example.assignedREDseq: an example assigned REDseq dataset
example.map: an example REmap dataset
example.REDseq: an example sequencing dataset from a restoration enzyme...
plotCutDistribution: plot cut frequencies of RE sites along a given chromosome
searchPattern: search pattern(s) in a genome
summarizeByRE: Output count/weight summary by restriction enzyme cut site ID...
summarizeBySeq: Output count/weight summary by sequences
writeHits: write the hits of pattern search to a bed file