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