Function reference • Repguide

Pipeline Functions for running the entire workflow
`addAlignments()`	Add multiple sequence alignment to guideSet object
`addCombinations()`	Add guideRNA combinations to guideSet object.
`addGuides()`	Add guideRNAs to guideSet object
`addTargets()`	Add targets to a guideSet object
`createGuideSet()`	Create new guideSet object
`clustGuides()`	Cluster guideRNAs
`selGuides()`	Blacklist guideRNAs
Import/Export/Accessors Functions for reading, writing and accessing guideSet objects
`blacklisted()`	Returns blacklisted regions from guideSet
`combinations()`	Returns blacklisted regions from guideSet
`export()`	Exports results from guideSet
`mappings()`	Returns genomic mappings from guideSet
`repnames()`	Returns transposable element families from guideSet
Visualization Functions for generating QC plots
`plotCombinations()`	Generates combinations QC plots
`plotGuides()`	Generates guides QC plots
`plotTargets()`	Generates targets QC plots
Datasets Datasets provided with the Repguide package
`essential_genes`	Essential human gene promoter coordinates
Classes Repguide S4 objects
`guideSet-class`	An S4 class to store genomic annotations and results of Repguide functions.

Reference