# Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks

## Documentation for package ‘craftgrn’ version 0.1.6

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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_tfbs | Predict transcription factor binding sites from matched footprint and RNA data
predict_tf_targets | Predict TF targets through TFBS-target and TF-target correlations
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