{ "_id": "6a1558c5acfb0bcc41d5eca2", "Package": "FastCCCR", "Type": "Package", "Title": "Fast Cell-Cell Communication Analysis with Statistical Framework", "Version": "1.0.0", "Date": "2026-01-26", "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\",\nemail = \"liuzaoqu@163.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5520-5765\")),\nperson(\"Wenjing\", \"Zhong\", role = \"ctb\"),\nperson(\"Marvin\", \"Yao\", role = \"ctb\")\n)", "Description": "A high-performance R package for cell-cell communication\n(CCC) analysis in single-cell RNA sequencing data. FastCCCR\nimplements an innovative statistical framework based on exact\nnull distribution computation, Cauchy combination of multiple\nstatistical methods, and reference-based inference. The package\nis optimized with Rcpp for computational efficiency and\nsupports both Seurat V4 and V5 objects. Key features include:\n(1) Multiple scoring methods with Cauchy combination, (2)\nReference panel construction and query inference, (3) Support\nfor multiple ligand-receptor databases (CellPhoneDB, CellChat,\nNicheNet), (4) High-performance vectorized and parallel\ncomputation.", "License": "MIT + file LICENSE", "URL": "https://zaoqu-liu.github.io/FastCCCR/,\nhttps://github.com/Zaoqu-Liu/FastCCCR", "BugReports": "https://github.com/Zaoqu-Liu/FastCCCR/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "SystemRequirements": "C++17", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Collate": "'RcppExports.R' 'globals.R' 'zzz.R' 'utils.R' 'distribution.R'\n'dist-iid-set.R' 'dist-complex.R' 'dist-lr.R'\n'data-preprocess.R' 'score.R' 'core.R' 'cauchy-combine.R'\n'build-reference.R' 'infer-query.R' 'visualize.R'\n'FastCCCR-package.R'", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-26 06:14:08 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/FastCCCR", "RemoteRef": "main", "RemoteSha": "e2454107b95439b3adb3114008e8fab419284898", "Packaged": { "Date": "2026-05-26 08:19:41 UTC", "User": "root" }, "Author": "Zaoqu Liu [aut, cre] (ORCID: ),\nWenjing Zhong [ctb],\nMarvin Yao [ctb]", "Maintainer": "Zaoqu Liu ", "MD5sum": "2d354ebc94b87f1eddf259e7fa0ae096", "_user": "zaoqu-liu", "_type": "src", "_file": "FastCCCR_1.0.0.tar.gz", "_fileid": "f81400866dfb4e872ba9d2468cbe86fa572ae77bf372bee3c919b203b0a73425", "_filesize": 1041695, "_sha256": "f81400866dfb4e872ba9d2468cbe86fa572ae77bf372bee3c919b203b0a73425", "_created": "2026-05-26T08:19:41.000Z", "_published": "2026-05-26T08:24:37.500Z", "_distro": "noble", "_jobs": [ { "job": 77834759050, "time": 203, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7212215508" }, { "job": 77834759003, "time": 206, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7212216365" }, { "job": 77834759012, "time": 195, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7212213275" }, { "job": 77834758999, "time": 195, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7212213082" }, { "job": 77834759735, "time": 105, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7212185348" }, { "job": 77834759016, "time": 232, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7212223822" }, { "job": 77834759088, "time": 124, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7212191062" }, { "job": 77834759051, "time": 254, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7212230973" }, { "job": 77834114011, "time": 254, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7212150474" }, { "job": 77834759014, "time": 168, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7212204296" }, { "job": 77834759025, "time": 167, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7212204440" }, { "job": 77834759026, "time": 220, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7212220736" }, { "job": 77834758994, "time": 225, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7212221814" } ], "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/Zaoqu-Liu/FastCCCR", "_commit": { "id": "e2454107b95439b3adb3114008e8fab419284898", "author": "Zaoqu-Liu ", "committer": "Zaoqu-Liu ", "message": "fix: use get_pmf_array() method instead of direct field access\n\n- Fixed: data.table::as.matrix -> as.matrix (not exported)\n- Fixed: $pmf_array direct access fails for lazy distributions\n- Must use $get_pmf_array() to ensure PMF is computed\n", "time": 1769408048 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "orcid": "0000-0002-5520-5765", "description": "AI4S", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "R6", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.0", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "future.apply", "role": "Imports" }, { "package": "progressr", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.0.0", "role": "Suggests" }, { "package": "SeuratObject", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "ComplexHeatmap", "role": "Suggests" }, { "package": "circlize", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "zaoqu-liu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 14 }, { "week": "2026-05", "n": 8 } ], "_tags": [], "_stars": 3, "_contributors": [ { "user": "zaoqu-liu", "count": 22, "uuid": 68080738 } ], "_userbio": { "uuid": 68080738, "type": "user", "name": "LIU Zaoqu", "description": "AI4S" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FastCCCR" }, "_devurl": "https://github.com/zaoqu-liu/fastcccr", "_pkgdown": "https://zaoqu-liu.github.io/FastCCCR/", "_searchresults": 6, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/FastCCCR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "analyze_interactions_percents", "batch_compute_gene_distributions_cpp", "batch_compute_pvalues_cpp", "build_reference", "calculate_cluster_mean", "calculate_cluster_mean_distribution", "calculate_cluster_means_cpp", "calculate_cluster_percents", "calculate_cluster_percents_cpp", "calculate_cluster_quantile", "calculate_cluster_quantile_distribution", "calculate_cluster_quantiles_cpp", "calculate_interaction_strengths_cpp", "calculate_interactions_pvalue", "calculate_interactions_strength", "cauchy_combine", "cauchy_combine_cpp", "cauchy_combine_files", "cauchy_combine_with_stat", "check_interactions_by_DEG", "cluster_markers_method", "combine_complex_distribution", "combine_complex_distribution_dt", "create_distribution", "create_significant_df", "digitize_transform_cpp", "Distribution", "fast_histogram_cpp", "fastccc", "fastccc_cauchy", "fft_convolve_cpp", "get_average_distribution", "get_count_data", "get_input_data", "get_input_data_from_files", "get_interactions", "get_minimum_distribution", "get_minimum_distribution_cpp", "get_network_data", "get_pmf_from_digit_samples", "get_pvalue", "get_pvalues_from_pmf_cpp", "get_strength_network_data", "get_threshold", "infer_query", "load_reference_config", "multiply_distributions_cpp", "plot_ccc_chord", "plot_ccc_heatmap", "plot_ccc_network", "statistical_analysis_method", "sum_distributions_cpp" ], "_help": [ { "page": "FastCCCR-package", "title": "FastCCCR: Fast Cell-Cell Communication Analysis", "topics": [ "FastCCCR-package", "FastCCCR" ] }, { "page": "analyze_interactions_percents", "title": "Analyze Interaction Percentages", "topics": [ "analyze_interactions_percents" ] }, { "page": "batch_compute_gene_distributions_cpp", "title": "Batch compute gene sum distributions", "topics": [ "batch_compute_gene_distributions_cpp" ] }, { "page": "batch_compute_pvalues_cpp", "title": "Batch compute p-values for L-R interactions", "topics": [ "batch_compute_pvalues_cpp" ] }, { "page": "build_reference", "title": "Build Reference Panel", "topics": [ "build_reference" ] }, { "page": "build-reference", "title": "Reference Building Functions", "topics": [ "build-reference" ] }, { "page": "calculate_cluster_mean", "title": "Calculate Cluster Mean Expression", "topics": [ "calculate_cluster_mean" ] }, { "page": "calculate_cluster_mean_distribution", "title": "Calculate Cluster Mean Distribution", "topics": [ "calculate_cluster_mean_distribution" ] }, { "page": "calculate_cluster_means_cpp", "title": "Calculate cluster means (vectorized)", "topics": [ "calculate_cluster_means_cpp" ] }, { "page": "calculate_cluster_percents", "title": "Calculate Cluster Expression Percentages", "topics": [ "calculate_cluster_percents" ] }, { "page": "calculate_cluster_percents_cpp", "title": "Calculate cluster expression percentages", "topics": [ "calculate_cluster_percents_cpp" ] }, { "page": "calculate_cluster_quantile", "title": "Calculate Cluster Quantile Expression", "topics": [ "calculate_cluster_quantile" ] }, { "page": "calculate_cluster_quantile_distribution", "title": "Calculate Cluster Quantile Distribution", "topics": [ "calculate_cluster_quantile_distribution" ] }, { "page": "calculate_cluster_quantiles_cpp", "title": "Calculate cluster quantiles (vectorized)", "topics": [ "calculate_cluster_quantiles_cpp" ] }, { "page": "calculate_interaction_strengths_cpp", "title": "Calculate interaction strengths (vectorized)", "topics": [ "calculate_interaction_strengths_cpp" ] }, { "page": "calculate_interactions_pvalue", "title": "Calculate Interaction P-values", "topics": [ "calculate_interactions_pvalue" ] }, { "page": "calculate_interactions_strength", "title": "Calculate Interaction Strengths", "topics": [ "calculate_interactions_strength" ] }, { "page": "cauchy_combine", "title": "Cauchy Combination of P-values", "topics": [ "cauchy_combine" ] }, { "page": "cauchy_combine_cpp", "title": "Cauchy combination of p-values", "topics": [ "cauchy_combine_cpp" ] }, { "page": "cauchy_combine_files", "title": "Cauchy Combine from Files", "topics": [ "cauchy_combine_files" ] }, { "page": "cauchy_combine_with_stat", "title": "Cauchy Combine with Statistic", "topics": [ "cauchy_combine_with_stat" ] }, { "page": "cauchy-combine", "title": "Cauchy Combination Functions", "topics": [ "cauchy-combine" ] }, { "page": "check_interactions_by_DEG", "title": "Check Interactions by DEG", "topics": [ "check_interactions_by_DEG" ] }, { "page": "cluster_markers_method", "title": "Cluster Markers Method", "topics": [ "cluster_markers_method" ] }, { "page": "combine_complex_distribution", "title": "Combine Complex Distribution", "topics": [ "combine_complex_distribution" ] }, { "page": "combine_complex_distribution_dt", "title": "Combine Complex Distribution", "topics": [ "combine_complex_distribution_dt" ] }, { "page": "core", "title": "Core Functions for FastCCCR", "topics": [ "core" ] }, { "page": "create_distribution", "title": "Create Distribution from Samples", "topics": [ "create_distribution" ] }, { "page": "create_significant_df", "title": "Create Significant Interactions DataFrame", "topics": [ "create_significant_df" ] }, { "page": "data-preprocess", "title": "Data Preprocessing Functions for FastCCCR", "topics": [ "data-preprocess" ] }, { "page": "digitize_transform_cpp", "title": "Digitize transform for rank-based analysis", "topics": [ "digitize_transform_cpp" ] }, { "page": "dist-complex", "title": "Complex Distribution Functions", "topics": [ "dist-complex" ] }, { "page": "dist-iid-set", "title": "IID Set Distribution Functions", "topics": [ "dist-iid-set" ] }, { "page": "dist-lr", "title": "L-R Distribution and P-value Functions", "topics": [ "dist-lr" ] }, { "page": "Distribution", "title": "Distribution Class for FastCCCR", "topics": [ "Distribution" ] }, { "page": "fast_histogram_cpp", "title": "Fast histogram for PMF computation", "topics": [ "fast_histogram_cpp" ] }, { "page": "fastccc", "title": "Simplified FastCCC Function", "topics": [ "fastccc" ] }, { "page": "fastccc_cauchy", "title": "FastCCC with Cauchy Combination", "topics": [ "fastccc_cauchy" ] }, { "page": "fft_convolve_cpp", "title": "FFT Convolution", "topics": [ "fft_convolve_cpp" ] }, { "page": "get_average_distribution", "title": "Get Average Distribution", "topics": [ "get_average_distribution" ] }, { "page": "get_count_data", "title": "Get Count Data Only", "topics": [ "get_count_data" ] }, { "page": "get_input_data", "title": "Get Input Data from Seurat Object", "topics": [ "get_input_data" ] }, { "page": "get_input_data_from_files", "title": "Load Data from Files", "topics": [ "get_input_data_from_files" ] }, { "page": "get_interactions", "title": "Get Interactions from Database", "topics": [ "get_interactions" ] }, { "page": "get_minimum_distribution", "title": "Get Minimum Distribution", "topics": [ "get_minimum_distribution" ] }, { "page": "get_minimum_distribution_cpp", "title": "Minimum Distribution", "topics": [ "get_minimum_distribution_cpp" ] }, { "page": "get_network_data", "title": "Get Network Data", "topics": [ "get_network_data" ] }, { "page": "get_pmf_from_digit_samples", "title": "Get PMF Array from Digitized Samples", "topics": [ "get_pmf_from_digit_samples" ] }, { "page": "get_pvalue", "title": "Get p-value from Distribution", "topics": [ "get_pvalue" ] }, { "page": "get_pvalues_from_pmf_cpp", "title": "Calculate P-values from PMF (vectorized)", "topics": [ "get_pvalues_from_pmf_cpp" ] }, { "page": "get_strength_network_data", "title": "Get Strength Network Data", "topics": [ "get_strength_network_data" ] }, { "page": "get_threshold", "title": "Get threshold from Distribution (for significance)", "topics": [ "get_threshold" ] }, { "page": "infer_query", "title": "Infer Query Using Reference", "topics": [ "infer_query" ] }, { "page": "infer-query", "title": "Query Inference Functions", "topics": [ "infer-query" ] }, { "page": "load_reference_config", "title": "Load Reference Config", "topics": [ "load_reference_config" ] }, { "page": "multiply_distributions_cpp", "title": "Multiply Distributions", "topics": [ "multiply_distributions_cpp" ] }, { "page": "plot_ccc_chord", "title": "Plot CCC Chord Diagram", "topics": [ "plot_ccc_chord" ] }, { "page": "plot_ccc_heatmap", "title": "Plot CCC Heatmap", "topics": [ "plot_ccc_heatmap" ] }, { "page": "plot_ccc_network", "title": "Plot CCC Network", "topics": [ "plot_ccc_network" ] }, { "page": "score", "title": "Score Calculation Functions for FastCCCR", "topics": [ "score" ] }, { "page": "statistical_analysis_method", "title": "FastCCC Single Method", "topics": [ "statistical_analysis_method" ] }, { "page": "sum_distributions_cpp", "title": "Sum Distributions (for average)", "topics": [ "sum_distributions_cpp" ] }, { "page": "visualize", "title": "Visualization Functions for FastCCCR", "topics": [ "visualize" ] } ], "_pkglogo": "https://github.com/Zaoqu-Liu/FastCCCR/raw/main/man/figures/logo.svg", "_readme": "https://github.com/Zaoqu-Liu/FastCCCR/raw/main/README.md", "_rundeps": [ "cli", "codetools", "data.table", "digest", "future", "future.apply", "globals", "lattice", "listenv", "Matrix", "parallelly", "progressr", "R6", "Rcpp", "RcppArmadillo", "rlang" ], "_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" } ], "_score": 2.4771212547196626, "_indexed": true, "_nocasepkg": "fastcccr", "_universes": [ "zaoqu-liu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T08:22:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "253ec6a94310336c98778d1a5c20dec1f92a63592db85c1edb6078df8b97f4a5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T08:22:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "40b90d4088c85ab0cd467b107a78b81d526cc2e33f71007c7f66ce0e3712e2f4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T08:22:47.000Z", "distro": "noble", "arch": "aarch64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "1721ea3b4d405c2201a0b7d2dfd75f8f62b33a4585a1b7694c22e5342dec5ded", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T08:22:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "a87b83a0dd34851d2a6edf0638867387a1052e35bf232e5b6c7811f4e6a25c4c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-26T08:21:26.000Z", "arch": "aarch64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "9bec9fbeac0573b67bf98c5498a99f3e3f968df4941fb618536a87b1e22c0c3f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-26T08:22:55.000Z", "arch": "x86_64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "06aa839c3283b39af2b877e47ff216ab6b0c36497ea1e239a0a9684f48ddc39d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-26T08:21:41.000Z", "arch": "aarch64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "b0244d909d2df526c1ec67fb73488b7658b7aafb7a12a5088ef90a6014864133", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-26T08:23:11.000Z", "arch": "x86_64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "ee2abd984893d9ca39451618dc174f4274b5749b26651b6fb51f0a19934914b3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-26T08:22:51.000Z", "arch": "emscripten", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "1de032da85dce4eaf0639f2b28c7f736d7da8953a39a95184f1df0173427b100", "status": "success", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-26T08:21:35.000Z", "arch": "x86_64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "2476786b9adb18c9948ed4421bb0fe7fa5d060aeb1b53974e99f7e9a82645559", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-26T08:22:31.000Z", "arch": "x86_64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "cc9baaee8fcd49484d1e8bc6a6f6659c8f53078f20756d664d38b41d73dae964", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-26T08:22:33.000Z", "arch": "x86_64", "commit": "e2454107b95439b3adb3114008e8fab419284898", "fileid": "e91af349c65d0b3224974490cc6f43fe1cafba45da0b85505de232b53d29ae71", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26440677520" } ] }