| EnrichStep-class | Base class of this package |
| GenBackground | Generate background regions and reset the size of foreground... |
| GeneOntology | Gene ontology enrichment analysis for provided gene list |
| MotifsInRegions | Find motifs in all input sequence regions |
| Pipelines | ready-to-use pipelines |
| 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 |
| TissueOpennessConserve | Tissue's open conservation 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 |
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