scglue.genomics.cis_regulatory_ranking(gene2region, region2tf, genes, regions, tfs, region_lens=None, n_samples=1000, random_state=None)[source]

Generate cis-regulatory ranking between genes and transcription factors

  • gene2region (Graph) – A graph connecting genes to cis-regulatory regions

  • region2tf (Graph) – A graph connecting cis-regulatory regions to transcription factors

  • genes (typing.List[str]) – A list of genes

  • tfs (typing.List[str]) – A list of transcription factors

  • regions (typing.List[str]) – A list of cis-regulatory regions

  • region_lens (typing.Optional[typing.List[int]]) – Lengths of cis-regulatory regions (if not provided, it is assumed that all regions have the same length)

  • n_samples (int) – Number of random samples used to evaluate regulatory enrichment (setting this to 0 disables enrichment evaluation)

  • random_state (typing.Union[RandomState, int, None]) – Random state

Return type:



gene2tf_rank – Cis regulatory ranking between genes and transcription factors