Transcription Factor Enrichment Analysis for ATAC-seq

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Documentation for package ‘ATACseqTFEA’ version 1.11.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ATACseqTFEA-package	Transcription Factor Enrichment Analysis for ATAC-seq
$-method	The methods for TFEAresults-class
$<--method	The methods for TFEAresults-class
as-method	The methods for TFEAresults-class
ATACseqTFEA	Transcription Factor Enrichment Analysis for ATAC-seq
calWeights	Calculate the weights for binding score
cluster_PWMs	Data in extdata
coerce-method	The methods for TFEAresults-class
count5ends	Prepare counts matrix for enrichment analysis
countsNormalization	Normalize counts by width of count region
DBscore	Differential binding analysis
doTFEA	Transcription factor enrichment analysis
ESvolcanoplot	Plot enrichment score for one transcription factor
eventsFilter	Filter the RangedSummarizedExperiment objects
expandBindingSites	Prepare the genomic ranges for proximal and distal regions for counting
extdata	Data in extdata
getBindingSites	The methods for TFEAresults-class
getBindingSites-method	The methods for TFEAresults-class
getEnrichmentScore	The methods for TFEAresults-class
getEnrichmentScore-method	The methods for TFEAresults-class
getMotifID	The methods for TFEAresults-class
getMotifID-method	The methods for TFEAresults-class
getWeightedBindingScore	Calculate the weighted binding score
importFimoBindingSites	Prepare binding site by fimo results
plotES	Plot enrichment score for one transcription factor
prepareBindingSites	Prepare binding site for TFEA
PWMatrixList	Data in extdata
reduceByPercentage	Reduce by percentage of overlaps of GRanges object
show-method	The methods for TFEAresults-class
TFEA	Transcription factor enrichment analysis
TFEAresults	Class '"TFEAresults"'
TFEAresults-class	Class '"TFEAresults"'
TFEAresults-methods	The methods for TFEAresults-class
[[-method	The methods for TFEAresults-class
[[<--method	The methods for TFEAresults-class