Package index • craftgrn

App and configuration

Start the app and load project configuration files.

run_app(): Run the Shiny Application
load_config(): Load a CraftGRN YAML config into an environment
validate_config(): Validate config values
craftgrn_demo_data_info(): Return metadata for configured external CraftGRN demo data
download_craftgrn_demo_data(): Download and unpack configured external CraftGRN demo data

Load, save, and prepare matched ATAC and RNA inputs.

load_omics_data(): Load a multi-omic data object from disk
save_omics_data(): Save a multi-omic data object to disk
load_prep_multiomic_data(): Load and prepare the Module 1 multi-omic object

Work with motif resources, footprints, and TF-footprint correlations.

predict_tfbs(): Predict transcription factor binding sites from matched footprint and RNA data
module1_prepare_tfbs_inputs(): Prepare Module 1 TFBS prediction inputs
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
build_module1_qc_report(): Build a Module 1 QC HTML report

Load, export, and hand off Module 1 predicted TFBS.

Predict TF targets through TFBS-target and TF-target correlations.

predict_tf_targets(): Predict TF targets through TFBS-target and TF-target correlations
module2_identify_candidate_links(): Link TFs to potential target genes based on TFBS-TSS proximity or 3D interaction data
module2_correlate_tf_targets(): Correlate TF expression with target gene expression
module2_link_fp_targets(): Build restricted candidate FP-target links
module2_correlate_fp_targets(): Correlate FP score with target gene expression
module2_output_predicted_links(): Assemble, filter, and output final predicted TF-FP-target links
build_module2_qc_report(): Build a Module 2 QC HTML report

Load, query, validate, export, and report Module 2 predicted links.

load_predicted_links(): Load predicted links from Module 2
query_predicted_links(): Query specific links by TF(s) and/or distance to TSS
check_predicted_links(): Perform sanity check for predicted links for Module 2 diagnostics
export_tf_target_bedpe(): Export predicted TF-target links as BEDPE
report_top_tf_targets(): Export an interactive HTML browser of individual TF regulons
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

Build topic inputs, train models, extract topics, and review Module 3 outputs.

run_topic_modeling(): Run topic modeling
module3_prepare_differential_links(): Prepare differential links for Module 3
module3_construct_docs(): Construct input documents for topic modeling
module3_train_topic_models(): Train Module 3 topic models
module3_extract_topics(): Extract Module 3 regulatory topics
build_module3_qc_report(): Build a Module 3 QC HTML report

Export standard Module 3 topic and differential GRN browsers.

visualize_topic_modeling_results(): Export interactive HTML browsers of topic modeling results
visualize_differential_grns(): Export an interactive HTML browser of differential GRNs