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build_condition()
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Construct logical condition to query database |
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connect_database()
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Connect to the regulondb database |
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convert_to_biostrings()
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Function to convert output of regulondb queries to Biostrings objects |
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convert_to_granges()
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Function to convert output of regulondb queries to GenomicRanges objects |
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existing_intervals()
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Constructs a particular logical condition to query database |
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existing_partial_match()
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Constructs a logical condition to query database |
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get_binding_sites()
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Get the binding sites for a Transcription Factor (TF) |
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get_dataset()
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Extract data from RegulonDB |
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get_dna_objects()
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Retrieve genomic elements from regulonDB |
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get_gene_regulators()
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Get TFs or genes that regulate the genes of interest |
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get_gene_synonyms()
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Retrieve gene synonyms |
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get_regulatory_network()
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Return complete regulatory network. |
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get_regulatory_summary()
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Return summary of gene regulation. |
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guess_id()
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Guess gene id type |
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list_attributes()
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List attributes/fields from a dataset/table |
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list_datasets()
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List available datasets in RegulonDB database |
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non_existing_intervals()
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Constructs a logical condition to query database |
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plot_dna_objects()
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Plot annotation elements within genomic region |
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regulondb-class
|
The regulondb class |
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show(<regulondb>)
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Methods for regulondb objects |
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regulondb()
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Constructor function of a regulondb class |
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regulondb_result-class
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The regulondb_results class |