# Transcription Factors Enrichment Analysis

## Documentation for package ‘enrichTF’ version 1.12.0

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

## Help Pages

enrichFindMotifsInRegions | Find motifs in all input sequence regions
enrichFindMotifsInRegions-method | Find motifs in all input sequence regions
enrichGenBackground | Generate background regions and reset the size of foreground regions
enrichGenBackground-method | Generate background regions and reset the size of foreground regions
enrichGeneOntology | Gene ontology enrichment analysis for provided gene list
enrichGeneOntology-method | Gene ontology enrichment analysis for provided gene list
enrichRegionConnectTargetGene | Connect regions with their target genes
enrichRegionConnectTargetGene-method | Connect regions with their target genes
enrichSingleSampleReport | Final report for single group of regions
enrichSingleSampleReport-method | Final report for single group of regions
EnrichStep-class | Base class of this package
enrichTFsEnrichInRegions | Test each TF is enriched in regions or not
enrichTFsEnrichInRegions-method | Test each TF is enriched in regions or not
enrichTissueOpennessConserve | Tissue's open conservation of the given region
enrichTissueOpennessConserve-method | Tissue's open conservation of the given region
enrichTissueOpennessSpecificity | Tissue's open specificity of the given region
enrichTissueOpennessSpecificity-method | Tissue's open specificity of the given region
enrichUnzipAndMergeBed | Unzip all zipped BED files and merge them into one BED file
enrichUnzipAndMergeBed-method | Unzip all zipped BED files and merge them into one BED file
findMotifsInRegions | Find motifs in all input sequence regions
GenBackground | Generate background regions and reset the size of foreground regions
genBackground | Generate background regions and reset the size of foreground regions
GeneOntology | Gene ontology enrichment analysis for provided gene list
geneOntology | Gene ontology enrichment analysis for provided gene list
GeneReguPipe | ready-to-use pipelines
MotifsInRegions | Find motifs in all input sequence regions
motifsInRegions | Find motifs in all input sequence regions
PECA_TF_enrich | ready-to-use pipelines
Pipelines | ready-to-use pipelines
RegionConnectTargetGene | Connect regions with their target genes
regionConnectTargetGene | Connect regions with their target genes
SingleSampleReport | Final report for single group of regions
TFsEnrichInRegions | Test each TF is enriched in regions or not
tfsEnrichInRegions | Test each TF is enriched in regions or not
TissueOpennessConserve | Tissue's open conservation of the given region
tissueOpennessConserve | Tissue's open conservation of the given region
TissueOpennessSpecificity | Tissue's open specificity of the given region
tissueOpennessSpecificity | Tissue's open specificity of the given region
UnzipAndMergeBed | Unzip all zipped BED files and merge them into one BED file
unzipAndMergeBed | Unzip all zipped BED files and merge them into one BED file