regutools: an R package for data extraction from RegulonDB

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Documentation for package ‘regutools’ version 1.21.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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