Package: craftgrn 0.1.6

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 available at <doi:10.1038/s41467-020-18035-1>, <https://www.jmlr.org/papers/v3/blei03a.html>, and <doi:10.48550/arXiv.1510.08628>.

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

craftgrn_0.1.6.tar.gz
craftgrn_0.1.6.tar.gz(r-4.7-arm64)craftgrn_0.1.6.tar.gz(r-4.7-x86_64)craftgrn_0.1.6.tar.gz(r-4.6-arm64)craftgrn_0.1.6.tar.gz(r-4.6-x86_64)
craftgrn_0.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
craftgrn/json (API)
NEWS

# Install 'craftgrn' in R:
install.packages('craftgrn', repos = c('https://cran.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:

Conda:

cppopenmp

2.70 score 2 scripts 40 exports 65 dependencies

Last updated from:33e8d3589c. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK321
linux-devel-x86_64OK321
source / vignettesOK382
linux-release-arm64OK333
linux-release-x86_64OK339
wasm-releaseOK255

Exports:build_module1_qc_reportbuild_module2_qc_reportbuild_module3_qc_reportcheck_predicted_linkscraftgrn_demo_data_infodownload_craftgrn_demo_dataexport_predicted_tfbs_bedexport_tf_target_bedpeload_configload_gene_tssload_omics_dataload_predicted_linksload_predicted_tfbsload_prep_multiomic_datamodule1_correlate_TF_to_canonical_tfbsmodule1_filter_canonical_bound_tfbsmodule1_predict_full_tfbsmodule1_prepare_tfbs_inputsmodule2_correlate_fp_targetsmodule2_correlate_tf_targetsmodule2_identify_candidate_linksmodule2_link_fp_targetsmodule2_output_predicted_linksmodule3_construct_docsmodule3_extract_topicsmodule3_prepare_differential_linksmodule3_train_topic_modelsoutput_predicted_tfbspredict_tf_targetspredict_tfbsquery_predicted_linksreport_direct_tf_tf_regulationsreport_tf_tf_coregulationsreport_top_tf_targetsrun_apprun_topic_modelingsave_omics_datavalidate_configvisualize_differential_grnsvisualize_topic_modeling_results

Dependencies:askpassbitbit64clicliprclustercodetoolsconfigcpp11crayoncurldata.tabledigestdplyrenrichRfarverfuturefuture.applygenericsggplot2globalsgluegtablehmshttrisobandjsonlitelabelingLDAvislifecyclelistenvmagrittrmimeopensslparallellypheatmappillarpkgconfigprettyunitsprogressproxypurrrR6RColorBrewerRcppreadrrjsonRJSONIOrlangS7scalesstringistringrsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrWriteXLSyaml

Get started with CraftGRN

Rendered fromcraftgrn.Rmdusingknitr::rmarkdownon Jun 18 2026.

Last update: 2026-06-18
Started: 2026-06-18

Readme and manuals

Help Manual

Help pageTopics
Build a Module 1 QC HTML reportbuild_module1_qc_report
Build a Module 2 QC HTML reportbuild_module2_qc_report
Build a Module 3 QC HTML reportbuild_module3_qc_report
Perform sanity check for predicted links for Module 2 diagnosticscheck_predicted_links
Return metadata for configured external CraftGRN demo datacraftgrn_demo_data_info
Download and unpack configured external CraftGRN demo datadownload_craftgrn_demo_data
Export predicted TFBS as BED filesexport_predicted_tfbs_bed
Export predicted TF-target links as BEDPEexport_tf_target_bedpe
Load a CraftGRN YAML config into an environmentload_config
Load a multi-omic data object from diskload_omics_data
Load predicted links from Module 2load_predicted_links
Load TFBS predicted from Module 1load_predicted_tfbs
Load and prepare the Module 1 multi-omic objectload_prep_multiomic_data
Correlate TFs to their canonical TFBSmodule1_correlate_TF_to_canonical_tfbs
Filter footprints with canonical binding for full TFBS predictionmodule1_filter_canonical_bound_tfbs
Predict full TFBS for all expressed TFsmodule1_predict_full_tfbs
Prepare Module 1 TFBS prediction inputsmodule1_prepare_tfbs_inputs
Correlate FP score with target gene expressionmodule2_correlate_fp_targets
Correlate TF expression with target gene expressionmodule2_correlate_tf_targets
Link TFs to potential target genes based on TFBS-TSS proximity or 3D interaction datamodule2_identify_candidate_links
Build restricted candidate FP-target linksmodule2_link_fp_targets
Assemble, filter, and output final predicted TF-FP-target linksmodule2_output_predicted_links
Construct input documents for topic modelingmodule3_construct_docs
Extract Module 3 regulatory topicsmodule3_extract_topics
Prepare differential links for Module 3module3_prepare_differential_links
Train Module 3 topic modelsmodule3_train_topic_models
Output predicted TFBSoutput_predicted_tfbs
Predict TF targets through TFBS-target and TF-target correlationspredict_tf_targets
Predict transcription factor binding sites from matched footprint and RNA datapredict_tfbs
Query specific links by TF(s) and/or distance to TSSquery_predicted_links
Export an interactive HTML browser of direct TF-TF regulationsreport_direct_tf_tf_regulations
Export an interactive HTML browser of TF-TF co-regulatory activitiesreport_tf_tf_coregulations
Export an interactive HTML browser of individual TF regulonsreport_top_tf_targets
Run the Shiny Applicationrun_app
Run topic modelingrun_topic_modeling
Save a multi-omic data object to disksave_omics_data
Validate config valuesvalidate_config
Export an interactive HTML browser of differential GRNsvisualize_differential_grns
Export interactive HTML browsers of topic modeling resultsvisualize_topic_modeling_results