# Transcription Factor Enrichment Analysis for ATAC-seq

## Documentation for package ‘ATACseqTFEA’ version 1.12.0

- 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