Package: craftgrn 0.1.7

Yaoxiang Li

craftgrn: Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks

Provides a reproducible framework for constructing and comparing gene regulatory networks by integrating chromatin accessibility footprint scores with matched RNA expression data. It implements context-specific enhancer-gene linking, transcription factor focused network analysis, differential network analysis, and regulatory topic modeling workflows for systematic exploration of gene regulation across conditions. Methodological background is described in Bentsen and others (2020) <doi:10.1038/s41467-020-18035-1>, Blei, Ng and Jordan (2003) <https://www.jmlr.org/papers/v3/blei03a.html>, and Chen, Li, Zhu and Chen (2015) <doi:10.48550/arXiv.1510.08628>.

Authors:Yaoxiang Li [aut, cre], Chunling Yi [aut]

craftgrn_0.1.7.tar.gz
craftgrn_0.1.7.zip(r-4.7-x86_64)craftgrn_0.1.7.zip(r-4.7-arm64)craftgrn_0.1.7.zip(r-4.6-x86_64)craftgrn_0.1.7.zip(r-4.6-arm64)craftgrn_0.1.7.zip(r-4.5-x86_64)
craftgrn_0.1.7.tgz(r-4.6-x86_64)craftgrn_0.1.7.tgz(r-4.6-arm64)craftgrn_0.1.7.tgz(r-4.5-x86_64)craftgrn_0.1.7.tgz(r-4.5-arm64)
craftgrn_0.1.7.tar.gz(r-4.7-arm64)craftgrn_0.1.7.tar.gz(r-4.7-x86_64)craftgrn_0.1.7.tar.gz(r-4.6-arm64)craftgrn_0.1.7.tar.gz(r-4.6-x86_64)
craftgrn_0.1.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
craftgrn/json (API)

# Install 'craftgrn' in R:

install.packages('craftgrn', repos = c('https://oncologylab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/oncologylab/craftgrn/issues

Pkgdown/docs site:https://oncologylab.github.io

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

atac-seq bioinformatics chromatin-accessibility computational-biology gene-regulation gene-regulation-networks multiomics network-inference regulatory-genomics rna-seq topic-modeling transcription-factors cpp openmp

7.82 score 510 stars 2 scripts 507 downloads 46 exports 63 dependencies

Last updated from:b905506ec0. Checks:13 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	526
linux-devel-x86_64	ERROR	603
source / vignettes	OK	429
linux-release-arm64	ERROR	481
linux-release-x86_64	ERROR	584
macos-release-arm64	ERROR	778
macos-release-x86_64	ERROR	950
macos-oldrel-arm64	ERROR	740
macos-oldrel-x86_64	ERROR	857
windows-devel-arm64	ERROR	766
windows-devel-x86_64	ERROR	643
windows-release-arm64	ERROR	800
windows-release-x86_64	ERROR	649
windows-oldrel-x86_64	ERROR	738
wasm-release	OK	288

Exports:build_module1_qc_report build_module1_tfbs_explorer build_module2_qc_report build_module3_qc_report build_tfbs_umap_report check_predicted_links craftgrn_demo_data_info download_craftgrn_demo_data export_predicted_tfbs_bed export_tf_target_bedpe load_config load_gene_tss load_omics_data load_predicted_links load_predicted_tfbs load_prep_multiomic_data module1_correlate_TF_to_canonical_tfbs module1_filter_canonical_bound_tfbs module1_predict_full_tfbs module1_prepare_tfbs_inputs module2_correlate_fp_targets module2_correlate_tf_targets module2_identify_candidate_links module2_link_fp_targets module2_output_predicted_links module3_construct_docs module3_extract_topics module3_prepare_condition_links module3_prepare_differential_links module3_train_topic_models output_predicted_tfbs plot_tf_tf_cobinding_heatmap plot_tfbs_condition_comparison predict_tf_targets predict_tfbs query_predicted_links report_direct_tf_tf_regulations report_tf_tf_coregulations report_top_tf_targets resolve_gene_symbols run_app run_topic_modeling save_omics_data validate_config visualize_differential_grns visualize_topic_modeling_results

Dependencies:askpass bit bit64 cli clipr cluster codetools config cpp11 crayon curl data.table digest dplyr enrichly enrichR farver future future.apply generics ggplot2 globals glue gtable hms httr isoband jsonlite labeling lifecycle listenv magrittr mime openssl parallelly pheatmap pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp readr rjson rlang S7 scales stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr WriteXLS yaml

Get started with CraftGRN

Rendered fromcraftgrn.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-03-23

Help page	Topics
Build a Module 1 QC HTML report	build_module1_qc_report
Build the interactive Module 1 TFBS Explorer	build_module1_tfbs_explorer
Build a Module 2 QC HTML report	build_module2_qc_report
Build a Module 3 QC HTML report	build_module3_qc_report
Build an interactive TF UMAP report from predicted TFBS	build_tfbs_umap_report
Perform sanity check for predicted links for Module 2 diagnostics	check_predicted_links
Return metadata for configured external CraftGRN demo data	craftgrn_demo_data_info
Download and unpack configured external CraftGRN demo data	download_craftgrn_demo_data
Export predicted TFBS as BED files	export_predicted_tfbs_bed
Export predicted TF-target links as BEDPE	export_tf_target_bedpe
Load a CraftGRN YAML config into an environment	load_config
Load a multi-omic data object from disk	load_omics_data
Load predicted links from Module 2	load_predicted_links
Load TFBS predicted from Module 1	load_predicted_tfbs
Load and prepare the Module 1 multi-omic object	load_prep_multiomic_data
Correlate TFs to their canonical TFBS	module1_correlate_TF_to_canonical_tfbs
Filter footprints with canonical binding for full TFBS prediction	module1_filter_canonical_bound_tfbs
Predict full TFBS for all expressed TFs	module1_predict_full_tfbs
Prepare Module 1 TFBS prediction inputs	module1_prepare_tfbs_inputs
Correlate FP score with target gene expression	module2_correlate_fp_targets
Correlate TF expression with target gene expression	module2_correlate_tf_targets
Link TFs to potential target genes based on TFBS-TSS proximity or 3D interaction data	module2_identify_candidate_links
Build restricted candidate FP-target links	module2_link_fp_targets
Assemble, filter, and output final predicted TF-FP-target links	module2_output_predicted_links
Construct input documents for topic modeling	module3_construct_docs
Extract Module 3 regulatory topics	module3_extract_topics
Prepare condition-native Module 3 links	module3_prepare_condition_links
Prepare differential links for Module 3	module3_prepare_differential_links
Train Module 3 topic models	module3_train_topic_models
Output predicted TFBS	output_predicted_tfbs
Plot a TF-TF co-binding heatmap	plot_tf_tf_cobinding_heatmap
Plot TFBS changes between two conditions	plot_tfbs_condition_comparison
Predict TF targets through TFBS-target and TF-target correlations	predict_tf_targets
Predict transcription factor binding sites from matched footprint and RNA data	predict_tfbs
Query specific links by TF(s) and/or distance to TSS	query_predicted_links
Export an interactive HTML browser of direct TF-TF regulations	report_direct_tf_tf_regulations
Export an interactive HTML browser of TF-TF co-regulatory activities	report_tf_tf_coregulations
Export an interactive HTML browser of individual TF regulons	report_top_tf_targets
Resolve gene symbols to formal species-specific symbols	resolve_gene_symbols
Run the Shiny Application	run_app
Run topic modeling	run_topic_modeling
Save a multi-omic data object to disk	save_omics_data
Validate config values	validate_config
Export an interactive HTML browser of differential GRNs	visualize_differential_grns
Export interactive HTML browsers of topic modeling results	visualize_topic_modeling_results

Package: craftgrn 0.1.7

craftgrn: Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks

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