{ "_id": "6a346f0e3efcd9bda43c5514", "Package": "craftgrn", "Title": "Integrative Chromatin Accessibility and RNA Framework for Gene\nRegulatory Networks", "Version": "0.1.6", "Authors@R": "c(\nperson(\"Yaoxiang\", \"Li\", , \"liyaoxiang@outlook.com\", role = c(\"aut\", \"cre\")),\nperson(\"Chunling\", \"Yi\", role = \"aut\")\n)", "Description": "Provides a reproducible framework for constructing and\ncomparing gene regulatory networks by integrating chromatin\naccessibility footprint scores with matched RNA expression\ndata. It implements context-specific enhancer-gene linking,\ntranscription factor focused network analysis, differential\nnetwork analysis, and regulatory topic modeling workflows for\nsystematic exploration of gene regulation across conditions.\nMethodological background is available at\n,\n, and\n.", "License": "GPL (>= 3)", "VignetteBuilder": "knitr", "SystemRequirements": "Optional Shiny app support on Linux may require\nlibuv headers, for example libuv1-dev, or cmake for bundled\nlibuv builds in transitive dependencies.", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.3", "URL": "https://oncologylab.github.io/craftgrn/,\nhttps://github.com/oncologylab/craftgrn", "BugReports": "https://github.com/oncologylab/craftgrn/issues", "Config/Needs/website": "r-lib/pkgdown, tidyverse/tidytemplate", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-18 22:13:20 UTC", "User": "root" }, "Author": "Yaoxiang Li [aut, cre], Chunling Yi [aut]", "Maintainer": "Yaoxiang Li ", "Config/pak/sysreqs": "cmake libuv1-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-06-18 16:50:08 UTC", "RemoteUrl": "https://github.com/cran/craftgrn", "RemoteRef": "HEAD", "RemoteSha": "33e8d3589c5837d32b687e5357100372775a60b1", "MD5sum": "0e695469cefe0030f33046e78df1781e", "_user": "cran", "_type": "src", "_file": "craftgrn_0.1.6.tar.gz", "_fileid": "e821ea5c815ffb55efbf25aa5aa9843d4036e374fb8b68fd6654ddd9d1b4d464", "_filesize": 934176, "_sha256": "e821ea5c815ffb55efbf25aa5aa9843d4036e374fb8b68fd6654ddd9d1b4d464", "_created": "2026-06-18T22:13:20.000Z", "_published": "2026-06-18T22:19:58.026Z", "_distro": "noble", "_jobs": [ { "job": 82244991134, "time": 321, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7737147345" }, { "job": 82244991126, "time": 321, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7737146482" }, { "job": 82244991147, "time": 333, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7737150498" }, { "job": 82244991208, "time": 339, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7737151099" }, { "job": 82244039591, "time": 382, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7737057234" }, { "job": 82244991115, "time": 255, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7737128470" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/27792296992", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/craftgrn", "_commit": { "id": "33e8d3589c5837d32b687e5357100372775a60b1", "author": "Yaoxiang Li ", "committer": "cran-robot ", "message": "version 0.1.6\n", "time": 1781801408 }, "_maintainer": { "name": "Yaoxiang Li", "email": "liyaoxiang@outlook.com", "login": "yaoxiangli", "description": "The most beautiful thing we can experience is the mysterious. It is the source of all true art and science.", "uuid": 18198096 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "cli", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "config", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "future.apply", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "enrichR", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "LDAvis", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "yaml", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "arrow", "role": "Suggests" }, { "package": "EnsDb.Hsapiens.v86", "role": "Suggests" }, { "package": "EnsDb.Mmusculus.v79", "role": "Suggests" }, { "package": "fgsea", "role": "Suggests" }, { "package": "golem", "role": "Suggests" }, { "package": "ggraph", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "gtable", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "htmlwidgets", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "msigdbr", "role": "Suggests" }, { "package": "parallelly", "role": "Suggests" }, { "package": "progressr", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rstudioapi", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-25", "n": 1 } ], "_tags": [ { "name": "0.1.6", "date": "2026-06-18" } ], "_stars": 0, "_contributors": [ { "user": "yaoxiangli", "count": 1, "uuid": 18198096 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 610, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/craftgrn" }, "_devurl": "https://github.com/oncologylab/craftgrn", "_pkgdown": "https://oncologylab.github.io/craftgrn/", "_searchresults": 2, "_topics": [ "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/craftgrn.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.1.6", "date": "2026-06-18" } ], "_exports": [ "build_module1_qc_report", "build_module2_qc_report", "build_module3_qc_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_differential_links", "module3_train_topic_models", "output_predicted_tfbs", "predict_tf_targets", "predict_tfbs", "query_predicted_links", "report_direct_tf_tf_regulations", "report_tf_tf_coregulations", "report_top_tf_targets", "run_app", "run_topic_modeling", "save_omics_data", "validate_config", "visualize_differential_grns", "visualize_topic_modeling_results" ], "_help": [ { "page": "build_module1_qc_report", "title": "Build a Module 1 QC HTML report", "topics": [ "build_module1_qc_report" ] }, { "page": "build_module2_qc_report", "title": "Build a Module 2 QC HTML report", "topics": [ "build_module2_qc_report" ] }, { "page": "build_module3_qc_report", "title": "Build a Module 3 QC HTML report", "topics": [ "build_module3_qc_report" ] }, { "page": "check_predicted_links", "title": "Perform sanity check for predicted links for Module 2 diagnostics", "topics": [ "check_predicted_links" ] }, { "page": "craftgrn_demo_data_info", "title": "Return metadata for configured external CraftGRN demo data", "topics": [ "craftgrn_demo_data_info" ] }, { "page": "download_craftgrn_demo_data", "title": "Download and unpack configured external CraftGRN demo data", "topics": [ "download_craftgrn_demo_data" ] }, { "page": "export_predicted_tfbs_bed", "title": "Export predicted TFBS as BED files", "topics": [ "export_predicted_tfbs_bed" ] }, { "page": "export_tf_target_bedpe", "title": "Export predicted TF-target links as BEDPE", "topics": [ "export_tf_target_bedpe" ] }, { "page": "load_config", "title": "Load a CraftGRN YAML config into an environment", "topics": [ "load_config" ] }, { "page": "load_omics_data", "title": "Load a multi-omic data object from disk", "topics": [ "load_omics_data" ] }, { "page": "load_predicted_links", "title": "Load predicted links from Module 2", "topics": [ "load_predicted_links" ] }, { "page": "load_predicted_tfbs", "title": "Load TFBS predicted from Module 1", "topics": [ "load_predicted_tfbs" ] }, { "page": "load_prep_multiomic_data", "title": "Load and prepare the Module 1 multi-omic object", "topics": [ "load_prep_multiomic_data" ] }, { "page": "module1_correlate_TF_to_canonical_tfbs", "title": "Correlate TFs to their canonical TFBS", "topics": [ "module1_correlate_TF_to_canonical_tfbs" ] }, { "page": "module1_filter_canonical_bound_tfbs", "title": "Filter footprints with canonical binding for full TFBS prediction", "topics": [ "module1_filter_canonical_bound_tfbs" ] }, { "page": "module1_predict_full_tfbs", "title": "Predict full TFBS for all expressed TFs", "topics": [ "module1_predict_full_tfbs" ] }, { "page": "module1_prepare_tfbs_inputs", "title": "Prepare Module 1 TFBS prediction inputs", "topics": [ "module1_prepare_tfbs_inputs" ] }, { "page": "module2_correlate_fp_targets", "title": "Correlate FP score with target gene expression", "topics": [ "module2_correlate_fp_targets" ] }, { "page": "module2_correlate_tf_targets", "title": "Correlate TF expression with target gene expression", "topics": [ "module2_correlate_tf_targets" ] }, { "page": "module2_identify_candidate_links", "title": "Link TFs to potential target genes based on TFBS-TSS proximity or 3D interaction data", "topics": [ "module2_identify_candidate_links" ] }, { "page": "module2_link_fp_targets", "title": "Build restricted candidate FP-target links", "topics": [ "module2_link_fp_targets" ] }, { "page": "module2_output_predicted_links", "title": "Assemble, filter, and output final predicted TF-FP-target links", "topics": [ "module2_output_predicted_links" ] }, { "page": "module3_construct_docs", "title": "Construct input documents for topic modeling", "topics": [ "module3_construct_docs" ] }, { "page": "module3_extract_topics", "title": "Extract Module 3 regulatory topics", "topics": [ "module3_extract_topics" ] }, { "page": "module3_prepare_differential_links", "title": "Prepare differential links for Module 3", "topics": [ "module3_prepare_differential_links" ] }, { "page": "module3_train_topic_models", "title": "Train Module 3 topic models", "topics": [ "module3_train_topic_models" ] }, { "page": "output_predicted_tfbs", "title": "Output predicted TFBS", "topics": [ "output_predicted_tfbs" ] }, { "page": "predict_tf_targets", "title": "Predict TF targets through TFBS-target and TF-target correlations", "topics": [ "predict_tf_targets" ] }, { "page": "predict_tfbs", "title": "Predict transcription factor binding sites from matched footprint and RNA data", "topics": [ "predict_tfbs" ] }, { "page": "query_predicted_links", "title": "Query specific links by TF(s) and/or distance to TSS", "topics": [ "query_predicted_links" ] }, { "page": "report_direct_tf_tf_regulations", "title": "Export an interactive HTML browser of direct TF-TF regulations", "topics": [ "report_direct_tf_tf_regulations" ] }, { "page": "report_tf_tf_coregulations", "title": "Export an interactive HTML browser of TF-TF co-regulatory activities", "topics": [ "report_tf_tf_coregulations" ] }, { "page": "report_top_tf_targets", "title": "Export an interactive HTML browser of individual TF regulons", "topics": [ "report_top_tf_targets" ] }, { "page": "run_app", "title": "Run the Shiny Application", "topics": [ "run_app" ] }, { "page": "run_topic_modeling", "title": "Run topic modeling", "topics": [ "run_topic_modeling" ] }, { "page": "save_omics_data", "title": "Save a multi-omic data object to disk", "topics": [ "save_omics_data" ] }, { "page": "validate_config", "title": "Validate config values", "topics": [ "validate_config" ] }, { "page": "visualize_differential_grns", "title": "Export an interactive HTML browser of differential GRNs", "topics": [ "visualize_differential_grns" ] }, { "page": "visualize_topic_modeling_results", "title": "Export interactive HTML browsers of topic modeling results", "topics": [ "visualize_topic_modeling_results" ] } ], "_pkglogo": "https://github.com/cran/craftgrn/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/cran/craftgrn/raw/HEAD/README.md", "_rundeps": [ "askpass", "bit", "bit64", "cli", "clipr", "cluster", "codetools", "config", "cpp11", "crayon", "curl", "data.table", "digest", "dplyr", "enrichR", "farver", "future", "future.apply", "generics", "ggplot2", "globals", "glue", "gtable", "hms", "httr", "isoband", "jsonlite", "labeling", "LDAvis", "lifecycle", "listenv", "magrittr", "mime", "openssl", "parallelly", "pheatmap", "pillar", "pkgconfig", "prettyunits", "progress", "proxy", "purrr", "R6", "RColorBrewer", "Rcpp", "readr", "rjson", "RJSONIO", "rlang", "S7", "scales", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "WriteXLS", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "craftgrn.Rmd", "filename": "craftgrn.html", "title": "Get started with CraftGRN", "engine": "knitr::rmarkdown", "headings": [ "Demo data", "Module 1: Predict TF binding sites", "Inputs", "Run Module 1", "Outputs", "Module 2: Connect TFs to target genes", "Process", "Module 3: Learn regulatory topics and visualize differential GRNs", "Run regulatory topics", "Review topic modeling and differential GRNs", "Next steps" ], "created": "2026-06-18 16:50:08", "modified": "2026-06-18 16:50:08", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": false, "_nocasepkg": "craftgrn", "_universes": [ "cran", "yaoxiangli", "oncologylab" ], "_indexurl": "https://oncologylab.r-universe.dev/craftgrn", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.6", "date": "2026-06-18T22:17:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "33e8d3589c5837d32b687e5357100372775a60b1", "fileid": "4283312b5065e2bdd4c804be8f5e6b35a153968df0daa2dcbacd825b03433f5f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27792296992" }, { "r": "4.7.0", "os": "linux", "version": "0.1.6", "date": "2026-06-18T22:17:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "33e8d3589c5837d32b687e5357100372775a60b1", "fileid": "dd81c1f539927bf9a8f52de7fb74d8c4ab3745a52cf5388b14974be85e4a00f0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27792296992" }, { "r": "4.6.0", "os": "linux", "version": "0.1.6", "date": "2026-06-18T22:18:02.000Z", "distro": "noble", "arch": "aarch64", "commit": "33e8d3589c5837d32b687e5357100372775a60b1", "fileid": "09556ef0e1ee963fc19fe999b51f758af73c1fb7664bac9122ce1bfde1ea674c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27792296992" }, { "r": "4.6.0", "os": "linux", "version": "0.1.6", "date": "2026-06-18T22:17:58.000Z", "distro": "noble", "arch": "x86_64", "commit": "33e8d3589c5837d32b687e5357100372775a60b1", "fileid": "2d0938b877cfa04fa2d63b980e181871df5075e70b80238604d8a54e86f8a764", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27792296992" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.6", "date": "2026-06-18T22:18:10.000Z", "arch": "emscripten", "commit": "33e8d3589c5837d32b687e5357100372775a60b1", "fileid": "243b106b1cf27a86481227d92389fdf91e944f77776b2fc29bc282cb8c0215f9", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/27792296992" } ] }