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.