build_module1_qc_report
                        Build a Module 1 QC HTML report
build_module2_qc_report
                        Build a Module 2 QC HTML report
build_module3_qc_report
                        Build a Module 3 QC HTML report
check_predicted_links   Perform sanity check for predicted links for
                        Module 2 diagnostics
craftgrn_demo_data_info
                        Return metadata for configured external
                        CraftGRN demo data
download_craftgrn_demo_data
                        Download and unpack configured external
                        CraftGRN demo data
export_predicted_tfbs_bed
                        Export predicted TFBS as BED files
export_tf_target_bedpe
                        Export predicted TF-target links as BEDPE
load_config             Load a CraftGRN YAML config into an environment
load_omics_data         Load a multi-omic data object from disk
load_predicted_links    Load predicted links from Module 2
load_predicted_tfbs     Load TFBS predicted from Module 1
load_prep_multiomic_data
                        Load and prepare the Module 1 multi-omic object
module1_correlate_TF_to_canonical_tfbs
                        Correlate TFs to their canonical TFBS
module1_filter_canonical_bound_tfbs
                        Filter footprints with canonical binding for
                        full TFBS prediction
module1_predict_full_tfbs
                        Predict full TFBS for all expressed TFs
module1_prepare_tfbs_inputs
                        Prepare Module 1 TFBS prediction inputs
module2_correlate_fp_targets
                        Correlate FP score with target gene expression
module2_correlate_tf_targets
                        Correlate TF expression with target gene
                        expression
module2_identify_candidate_links
                        Link TFs to potential target genes based on
                        TFBS-TSS proximity or 3D interaction data
module2_link_fp_targets
                        Build restricted candidate FP-target links
module2_output_predicted_links
                        Assemble, filter, and output final predicted
                        TF-FP-target links
module3_construct_docs
                        Construct input documents for topic modeling
module3_extract_topics
                        Extract Module 3 regulatory topics
module3_prepare_differential_links
                        Prepare differential links for Module 3
module3_train_topic_models
                        Train Module 3 topic models
output_predicted_tfbs   Output predicted TFBS
predict_tf_targets      Predict TF targets through TFBS-target and
                        TF-target correlations
predict_tfbs            Predict transcription factor binding sites from
                        matched footprint and RNA data
query_predicted_links   Query specific links by TF(s) and/or distance
                        to TSS
report_direct_tf_tf_regulations
                        Export an interactive HTML browser of direct
                        TF-TF regulations
report_tf_tf_coregulations
                        Export an interactive HTML browser of TF-TF
                        co-regulatory activities
report_top_tf_targets   Export an interactive HTML browser of
                        individual TF regulons
run_app                 Run the Shiny Application
run_topic_modeling      Run topic modeling
save_omics_data         Save a multi-omic data object to disk
validate_config         Validate config values
visualize_differential_grns
                        Export an interactive HTML browser of
                        differential GRNs
visualize_topic_modeling_results
                        Export interactive HTML browsers of topic
                        modeling results
