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| 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 |
| enrichRegionConnectTargetGene | Connect regions with their target genes |
| enrichRegionConnectTargetGene-method | Connect regions with their target genes |
| 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 |
| 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 |
| MotifsInRegions | Find motifs in all input sequence regions |
| motifsInRegions | Find motifs in all input sequence regions |
| PECA_TF_enrich | TF enrichment with PECA model |
| RegionConnectTargetGene | Connect regions with their target genes |
| regionConnectTargetGene | Connect regions with their target genes |
| TFsEnrichInRegions | Test each TF is enriched in regions or not |
| tfsEnrichInRegions | Test each TF is enriched in regions or not |