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Elementolab/

ChIPseeqer GUI documentation

This page describes the GUI version (Graphical User Interface) of the ChIPseeqer framework.

Current version of the ChIPseeqerGUI supports the following functionalities:

Categories	GUI functionality	Command-line tool(s)
Peaks Identification	Load raw data	split_raw_data_files.pl
	Peak Detection	ChIPseeqer.bin
	Create Tracks	ChIPseeqerPeaksTrack/ ChIPseeqerMakeReadDensityTrack
Genomic Annotation	Promoters Summary	ChIPseeqerSummaryPromoters
	Genomic Distribution	ChIPseeqerAnnotate
	RNAGenes	ChIPseeqerRNAGenes
Non-genic Annotation	Compare with ENCODE datasets	ChIPseeqerNongenicAnnotate
	Find Repeats	ChIPseeqerNongenicAnnotate
	Find CpG islands	ChIPseeqerNongenicAnnotate
	Find Segmental Duplicates	ChIPseeqerNongenicAnnotate
Motif analysis	Find motif in peaks	ChIPseeqerMotifMatch
	De novo motif discovery (FIRE)	ChIPseeqerFIRE
Pathways analysis	Find peaks/genes with specific pathway	ChIPseeqerPathwayMatch
	Find all enriched pathways (iPAGE)	ChIPseeqeriPAGE
Conservation analysis	Compute conserv. scores	ChIPseeqerCons
Comparison tools	Compare peaks	CompareIntervals
	Compare genes	CompareGenes
	Compute Jaccard coefficient	ChIPseeqerComputeJaccardIndex