Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks

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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