{
  "_id": "6a142c0dacfb0bcc41d40d08",
  "Package": "CellOracleR",
  "Type": "Package",
  "Title": "In Silico Gene Perturbation Analysis with Single-Cell Data",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\")),\nperson(\"Kenji\", \"Kamimoto\", role = \"ctb\",\ncomment = \"Original CellOracle Python package author\"))",
  "Description": "An R implementation of the CellOracle framework for in\nsilico gene perturbation analysis and gene regulatory network\n(GRN) inference from single-cell RNA-seq data. Predicts cell\nstate transitions in response to transcription factor\nperturbations by combining GRN models with single-cell\nexpression data. Key features include motif analysis for base\nGRN construction, cluster-specific GRN inference using\nregularized regression, perturbation simulation with signal\npropagation, and comprehensive visualization of predicted cell\nfate changes. Based on the methodology described in Kamimoto et\nal. (2023) <doi:10.15252/msb.202211547>.",
  "URL": "https://github.com/Zaoqu-Liu/CellOracleR",
  "BugReports": "https://github.com/Zaoqu-Liu/CellOracleR/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "License": "Apache License (>= 2) | file LICENSE",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "C++17",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev",
  "Repository": "https://zaoqu-liu.r-universe.dev",
  "Date/Publication": "2026-01-24 20:11:44 UTC",
  "RemoteUrl": "https://github.com/Zaoqu-Liu/CellOracleR",
  "RemoteRef": "main",
  "RemoteSha": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-25 10:51:15 UTC",
    "User": "root"
  },
  "Author": "Zaoqu Liu [aut, cre],\nKenji Kamimoto [ctb] (Original CellOracle Python package author)",
  "Maintainer": "Zaoqu Liu <liuzaoqu@163.com>",
  "MD5sum": "1bcebdfb61a66397d624d5a028444881",
  "_user": "zaoqu-liu",
  "_type": "src",
  "_file": "CellOracleR_0.1.0.tar.gz",
  "_fileid": "1b68a6a168208986affc2c7330c94d0960293e69a6d5aa700800e9faa201f432",
  "_filesize": 7307958,
  "_sha256": "1b68a6a168208986affc2c7330c94d0960293e69a6d5aa700800e9faa201f432",
  "_created": "2026-05-25T10:51:15.000Z",
  "_published": "2026-05-25T11:01:33.560Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77699178427,
      "time": 329,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7196837404"
    },
    {
      "job": 77699178433,
      "time": 359,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7196845246"
    },
    {
      "job": 77699178405,
      "time": 317,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7196834807"
    },
    {
      "job": 77699178461,
      "time": 358,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7196844843"
    },
    {
      "job": 77699178372,
      "time": 215,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7196808737"
    },
    {
      "job": 77699178404,
      "time": 523,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7196884135"
    },
    {
      "job": 77699178421,
      "time": 172,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7196798667"
    },
    {
      "job": 77699178425,
      "time": 302,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7196830636"
    },
    {
      "job": 77698264473,
      "time": 440,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196756606"
    },
    {
      "job": 77699178420,
      "time": 283,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196826170"
    },
    {
      "job": 77699178354,
      "time": 284,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7196826463"
    },
    {
      "job": 77699178416,
      "time": 285,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7196826724"
    },
    {
      "job": 77699178399,
      "time": 292,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7196828613"
    }
  ],
  "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/Zaoqu-Liu/CellOracleR",
  "_commit": {
    "id": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
    "author": "Zaoqu-Liu <liuzaoqu@163.com>",
    "committer": "Zaoqu-Liu <liuzaoqu@163.com>",
    "message": "Fix R-universe build: remove invalid ORCID, move qs to Suggests with RDS fallback\n",
    "time": 1769285504
  },
  "_maintainer": {
    "name": "Zaoqu Liu",
    "email": "liuzaoqu@163.com",
    "login": "zaoqu-liu",
    "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": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "Seurat",
      "version": ">= 4.0.0",
      "role": "Imports"
    },
    {
      "package": "SeuratObject",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "progressr",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "FNN",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "qs",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "TFBSTools",
      "role": "Suggests"
    },
    {
      "package": "motifmatchr",
      "role": "Suggests"
    },
    {
      "package": "BSgenome",
      "role": "Suggests"
    },
    {
      "package": "GenomicRanges",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Suggests"
    },
    {
      "package": "IRanges",
      "role": "Suggests"
    },
    {
      "package": "S4Vectors",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "clusterProfiler",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "role": "Suggests"
    },
    {
      "package": "JASPAR2020",
      "role": "Suggests"
    },
    {
      "package": "viridis",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "ggraph",
      "role": "Suggests"
    },
    {
      "package": "irlba",
      "role": "Suggests"
    },
    {
      "package": "arrow",
      "role": "Suggests"
    },
    {
      "package": "reshape2",
      "role": "Suggests"
    },
    {
      "package": "e1071",
      "role": "Suggests"
    },
    {
      "package": "rstanarm",
      "role": "Suggests"
    },
    {
      "package": "networkD3",
      "role": "Suggests"
    },
    {
      "package": "htmlwidgets",
      "role": "Suggests"
    }
  ],
  "_owner": "zaoqu-liu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-04",
      "n": 10
    }
  ],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "zaoqu-liu",
      "count": 10,
      "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/CellOracleR"
  },
  "_devurl": "https://github.com/zaoqu-liu/celloracler",
  "_searchresults": 7,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CellOracleR.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "annotate_peaks",
    "build_coef_matrix_cpp",
    "build_knn_graph_cpp",
    "calculate_embedding_shift_cpp",
    "calculate_grid_arrows_cpp",
    "calculate_relative_ratio_cpp",
    "center_cols_cpp",
    "clean_transition_prob_cpp",
    "clip_to_range_cpp",
    "col_delta_cor_full_cpp",
    "col_delta_cor_partial_cpp",
    "colSds_cpp",
    "compare_networks",
    "compute_embedding_knn_subset_cpp",
    "compute_fate_probability",
    "compute_pseudotime",
    "correlation_to_transition_prob_cpp",
    "create_base_grn",
    "create_oracle",
    "create_perturb_condition",
    "create_tfinfo",
    "do_simulation_cpp",
    "export_network",
    "extract_expression",
    "extract_peaks_from_signac",
    "filter_links",
    "find_network_motifs",
    "fit_grn",
    "fit_grn_bagging",
    "fit_grn_coef_matrix",
    "gaussian_kernel_cpp",
    "get_bagging_ridge_coefs",
    "get_base_grn_from_cicero",
    "get_bayesian_ridge_coefs",
    "get_embedding",
    "get_links",
    "get_network_entropy",
    "get_network_score",
    "get_perturb_value",
    "identify_hubs",
    "knn_distances_to_weights_cpp",
    "knn_impute_cpp",
    "Links",
    "load_base_grn",
    "load_oracle",
    "load_tfinfo",
    "markov_simulate",
    "markov_walk_batch_cpp",
    "markov_walk_cpp",
    "Net",
    "network_summary",
    "normalize_flow_cpp",
    "Oracle",
    "pairwise_dist_cpp",
    "permute_rows_nsign_cpp",
    "plot_cluster",
    "plot_degree_distribution",
    "plot_gene_expression",
    "plot_network_graph",
    "plot_pseudotime",
    "plot_quiver",
    "plot_score_comparison",
    "plot_scores_as_rank",
    "plot_simulation_combined",
    "plot_simulation_flow",
    "plot_transition_sankey",
    "row_norms_cpp",
    "rowSds_cpp",
    "sankey",
    "save_oracle",
    "save_tfinfo",
    "scale_cols_cpp",
    "scan_motifs",
    "score_cv_vs_mean",
    "setup_parallel",
    "shortest_paths",
    "shuffle_coef_matrix_cpp",
    "simulate_shift",
    "simulation_summary",
    "summarize_trajectories",
    "TFinfo"
  ],
  "_help": [
    {
      "page": "annotate_peaks",
      "title": "Annotate peaks with nearby genes",
      "topics": [
        "annotate_peaks"
      ]
    },
    {
      "page": "build_coef_matrix_cpp",
      "title": "Build coefficient matrix from gene-wise results",
      "topics": [
        "build_coef_matrix_cpp"
      ]
    },
    {
      "page": "build_knn_graph_cpp",
      "title": "Build sparse connectivity matrix from KNN indices",
      "topics": [
        "build_knn_graph_cpp"
      ]
    },
    {
      "page": "calculate_embedding_shift_cpp",
      "title": "Calculate embedding shift from transition probability",
      "topics": [
        "calculate_embedding_shift_cpp"
      ]
    },
    {
      "page": "calculate_grid_arrows_cpp",
      "title": "Grid arrow computation",
      "topics": [
        "calculate_grid_arrows_cpp"
      ]
    },
    {
      "page": "calculate_relative_ratio_cpp",
      "title": "Calculate relative ratio for OOD detection",
      "topics": [
        "calculate_relative_ratio_cpp"
      ]
    },
    {
      "page": "center_cols_cpp",
      "title": "Center matrix columns",
      "topics": [
        "center_cols_cpp"
      ]
    },
    {
      "page": "clean_transition_prob_cpp",
      "title": "Handle NA and zero-sum rows in transition matrix",
      "topics": [
        "clean_transition_prob_cpp"
      ]
    },
    {
      "page": "clip_to_range_cpp",
      "title": "Clip delta_X to distribution range",
      "topics": [
        "clip_to_range_cpp"
      ]
    },
    {
      "page": "col_delta_cor_full_cpp",
      "title": "Compute full delta correlation matrix",
      "topics": [
        "col_delta_cor_full_cpp"
      ]
    },
    {
      "page": "col_delta_cor_partial_cpp",
      "title": "Compute column-wise delta correlation (partial neighbors)",
      "topics": [
        "col_delta_cor_partial_cpp"
      ]
    },
    {
      "page": "colSds_cpp",
      "title": "Column-wise standard deviation",
      "topics": [
        "colSds_cpp"
      ]
    },
    {
      "page": "compare_networks",
      "title": "Compare networks between clusters",
      "topics": [
        "compare_networks"
      ]
    },
    {
      "page": "compute_embedding_knn_subset_cpp",
      "title": "Compute embedding KNN with subset selection",
      "topics": [
        "compute_embedding_knn_subset_cpp"
      ]
    },
    {
      "page": "compute_fate_probability",
      "title": "Compute fate probability to terminal states",
      "topics": [
        "compute_fate_probability"
      ]
    },
    {
      "page": "compute_pseudotime",
      "title": "Compute pseudotime based on transition probability",
      "topics": [
        "compute_pseudotime"
      ]
    },
    {
      "page": "correlation_to_transition_prob_cpp",
      "title": "Calculate transition probability from correlation",
      "topics": [
        "correlation_to_transition_prob_cpp"
      ]
    },
    {
      "page": "create_base_grn",
      "title": "Create base GRN from scATAC-seq data",
      "topics": [
        "create_base_grn"
      ]
    },
    {
      "page": "create_oracle",
      "title": "Create Oracle object from Seurat",
      "topics": [
        "create_oracle"
      ]
    },
    {
      "page": "create_perturb_condition",
      "title": "Create perturbation condition",
      "topics": [
        "create_perturb_condition"
      ]
    },
    {
      "page": "create_tfinfo",
      "title": "Create TFinfo object from peak data",
      "topics": [
        "create_tfinfo"
      ]
    },
    {
      "page": "do_simulation_cpp",
      "title": "Simulate signal propagation in GRN (C++ implementation)",
      "topics": [
        "do_simulation_cpp"
      ]
    },
    {
      "page": "export_network",
      "title": "Export network to various formats",
      "topics": [
        "export_network"
      ]
    },
    {
      "page": "extract_expression",
      "title": "Extract expression matrix from Seurat object",
      "topics": [
        "extract_expression"
      ]
    },
    {
      "page": "extract_peaks_from_signac",
      "title": "Process ATAC-seq peaks from Signac",
      "topics": [
        "extract_peaks_from_signac"
      ]
    },
    {
      "page": "filter_links",
      "title": "Filter links by threshold",
      "topics": [
        "filter_links"
      ]
    },
    {
      "page": "find_network_motifs",
      "title": "Find network motifs",
      "topics": [
        "find_network_motifs"
      ]
    },
    {
      "page": "fit_grn",
      "title": "Fit GRN for perturbation simulation",
      "topics": [
        "fit_grn"
      ]
    },
    {
      "page": "fit_grn_bagging",
      "title": "Fit GRN with bagging (batch version)",
      "topics": [
        "fit_grn_bagging"
      ]
    },
    {
      "page": "fit_grn_coef_matrix",
      "title": "Fit GRN coefficient matrix (single Ridge regression)",
      "topics": [
        "fit_grn_coef_matrix"
      ]
    },
    {
      "page": "gaussian_kernel_cpp",
      "title": "Gaussian kernel on distance matrix",
      "topics": [
        "gaussian_kernel_cpp"
      ]
    },
    {
      "page": "get_bagging_ridge_coefs",
      "title": "Get Bagging Ridge coefficients for a single target gene",
      "topics": [
        "get_bagging_ridge_coefs"
      ]
    },
    {
      "page": "get_base_grn_from_cicero",
      "title": "Get base GRN from Cicero/ATAC data",
      "topics": [
        "get_base_grn_from_cicero"
      ]
    },
    {
      "page": "get_bayesian_ridge_coefs",
      "title": "Get Bayesian Ridge coefficients for a single target gene",
      "topics": [
        "get_bayesian_ridge_coefs"
      ]
    },
    {
      "page": "get_embedding",
      "title": "Get embedding from Seurat object",
      "topics": [
        "get_embedding"
      ]
    },
    {
      "page": "get_links",
      "title": "Get Links object for network analysis",
      "topics": [
        "get_links"
      ]
    },
    {
      "page": "get_network_entropy",
      "title": "Calculate network entropy",
      "topics": [
        "get_network_entropy"
      ]
    },
    {
      "page": "get_network_score",
      "title": "Calculate network scores",
      "topics": [
        "get_network_score"
      ]
    },
    {
      "page": "get_perturb_value",
      "title": "Get perturbation values from expression data",
      "topics": [
        "get_perturb_value"
      ]
    },
    {
      "page": "identify_hubs",
      "title": "Identify hub genes",
      "topics": [
        "identify_hubs"
      ]
    },
    {
      "page": "knn_distances_to_weights_cpp",
      "title": "Compute KNN connectivity weights from distances",
      "topics": [
        "knn_distances_to_weights_cpp"
      ]
    },
    {
      "page": "knn_impute_cpp",
      "title": "KNN imputation using precomputed neighbors",
      "topics": [
        "knn_impute_cpp"
      ]
    },
    {
      "page": "Links",
      "title": "Links Class for Network Analysis",
      "topics": [
        "Links"
      ]
    },
    {
      "page": "load_base_grn",
      "title": "Load pre-built base GRN",
      "topics": [
        "load_base_grn"
      ]
    },
    {
      "page": "load_oracle",
      "title": "Load Oracle object from file",
      "topics": [
        "load_oracle"
      ]
    },
    {
      "page": "load_tfinfo",
      "title": "Load TFinfo object from file",
      "topics": [
        "load_tfinfo"
      ]
    },
    {
      "page": "markov_simulate",
      "title": "Markov simulation of cell trajectories",
      "topics": [
        "markov_simulate"
      ]
    },
    {
      "page": "markov_walk_batch_cpp",
      "title": "Batch Markov simulation with duplication",
      "topics": [
        "markov_walk_batch_cpp"
      ]
    },
    {
      "page": "markov_walk_cpp",
      "title": "Markov chain random walk simulation",
      "topics": [
        "markov_walk_cpp"
      ]
    },
    {
      "page": "Net",
      "title": "Net Class for GRN Inference",
      "topics": [
        "Net"
      ]
    },
    {
      "page": "network_summary",
      "title": "Calculate network statistics summary",
      "topics": [
        "network_summary"
      ]
    },
    {
      "page": "normalize_flow_cpp",
      "title": "Normalize flow vectors",
      "topics": [
        "normalize_flow_cpp"
      ]
    },
    {
      "page": "Oracle",
      "title": "Oracle Class for In Silico Gene Perturbation Analysis",
      "topics": [
        "Oracle"
      ]
    },
    {
      "page": "pairwise_dist_cpp",
      "title": "Compute pairwise Euclidean distances",
      "topics": [
        "pairwise_dist_cpp"
      ]
    },
    {
      "page": "permute_rows_nsign_cpp",
      "title": "Permute rows with sign flip for randomization",
      "topics": [
        "permute_rows_nsign_cpp"
      ]
    },
    {
      "page": "plot_cluster",
      "title": "Plot cells by cluster",
      "topics": [
        "plot_cluster"
      ]
    },
    {
      "page": "plot_degree_distribution",
      "title": "Plot degree distribution",
      "topics": [
        "plot_degree_distribution"
      ]
    },
    {
      "page": "plot_gene_expression",
      "title": "Plot gene expression on embedding",
      "topics": [
        "plot_gene_expression"
      ]
    },
    {
      "page": "plot_network_graph",
      "title": "Plot GRN as network graph",
      "topics": [
        "plot_network_graph"
      ]
    },
    {
      "page": "plot_pseudotime",
      "title": "Plot pseudotime on embedding",
      "topics": [
        "plot_pseudotime"
      ]
    },
    {
      "page": "plot_quiver",
      "title": "Plot quiver (cell-level velocity arrows)",
      "topics": [
        "plot_quiver"
      ]
    },
    {
      "page": "plot_score_comparison",
      "title": "Compare network scores between clusters",
      "topics": [
        "plot_score_comparison"
      ]
    },
    {
      "page": "plot_scores_as_rank",
      "title": "Plot network scores as ranked bar plot",
      "topics": [
        "plot_scores_as_rank"
      ]
    },
    {
      "page": "plot_simulation_combined",
      "title": "Create combined simulation plot",
      "topics": [
        "plot_simulation_combined"
      ]
    },
    {
      "page": "plot_simulation_flow",
      "title": "Plot perturbation simulation vector field",
      "topics": [
        "plot_simulation_flow"
      ]
    },
    {
      "page": "plot_transition_sankey",
      "title": "Create Sankey diagram from Oracle transition results",
      "topics": [
        "plot_transition_sankey"
      ]
    },
    {
      "page": "print.Links",
      "title": "Print method for Links",
      "topics": [
        "print.Links"
      ]
    },
    {
      "page": "print.Net",
      "title": "Print method for Net",
      "topics": [
        "print.Net"
      ]
    },
    {
      "page": "print.Oracle",
      "title": "Print method for Oracle",
      "topics": [
        "print.Oracle"
      ]
    },
    {
      "page": "print.TFinfo",
      "title": "Print method for TFinfo",
      "topics": [
        "print.TFinfo"
      ]
    },
    {
      "page": "row_norms_cpp",
      "title": "Row-wise L2 norm",
      "topics": [
        "row_norms_cpp"
      ]
    },
    {
      "page": "rowSds_cpp",
      "title": "Row-wise standard deviation",
      "topics": [
        "rowSds_cpp"
      ]
    },
    {
      "page": "save_oracle",
      "title": "Save Oracle object",
      "topics": [
        "save_oracle"
      ]
    },
    {
      "page": "save_tfinfo",
      "title": "Save TFinfo object",
      "topics": [
        "save_tfinfo"
      ]
    },
    {
      "page": "scale_cols_cpp",
      "title": "Scale matrix columns",
      "topics": [
        "scale_cols_cpp"
      ]
    },
    {
      "page": "scan_motifs",
      "title": "Scan peaks for TF motifs",
      "topics": [
        "scan_motifs"
      ]
    },
    {
      "page": "score_cv_vs_mean",
      "title": "Score CV vs Mean for variable gene selection",
      "topics": [
        "score_cv_vs_mean"
      ]
    },
    {
      "page": "setup_parallel",
      "title": "Setup parallel backend",
      "topics": [
        "setup_parallel"
      ]
    },
    {
      "page": "shortest_paths",
      "title": "Calculate shortest paths between genes",
      "topics": [
        "shortest_paths"
      ]
    },
    {
      "page": "shuffle_coef_matrix_cpp",
      "title": "Shuffle coefficient matrix for randomization control",
      "topics": [
        "shuffle_coef_matrix_cpp"
      ]
    },
    {
      "page": "simulate_shift",
      "title": "Simulate gene perturbation shift",
      "topics": [
        "simulate_shift"
      ]
    },
    {
      "page": "simulation_summary",
      "title": "Summary of simulation results",
      "topics": [
        "simulation_summary"
      ]
    },
    {
      "page": "summarize_trajectories",
      "title": "Summarize Markov simulation trajectories",
      "topics": [
        "summarize_trajectories"
      ]
    },
    {
      "page": "TFinfo",
      "title": "TFinfo Class for Motif Analysis",
      "topics": [
        "TFinfo"
      ]
    },
    {
      "page": "visualization",
      "title": "Visualization Functions",
      "topics": [
        "visualization"
      ]
    }
  ],
  "_readme": "https://github.com/Zaoqu-Liu/CellOracleR/raw/main/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "BH",
    "bitops",
    "bslib",
    "cachem",
    "caTools",
    "cli",
    "cluster",
    "codetools",
    "commonmark",
    "cowplot",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "deldir",
    "digest",
    "dotCall64",
    "dplyr",
    "dqrng",
    "evaluate",
    "farver",
    "fastDummies",
    "fastmap",
    "fitdistrplus",
    "FNN",
    "fontawesome",
    "foreach",
    "fs",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "ggrepel",
    "ggridges",
    "glmnet",
    "globals",
    "glue",
    "goftest",
    "gplots",
    "gridExtra",
    "gtable",
    "gtools",
    "here",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "ica",
    "igraph",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "listenv",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "memoise",
    "mime",
    "miniUI",
    "nlme",
    "openssl",
    "otel",
    "parallelly",
    "patchwork",
    "pbapply",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "progressr",
    "promises",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "RcppProgress",
    "RcppTOML",
    "reshape2",
    "reticulate",
    "rlang",
    "rmarkdown",
    "ROCR",
    "rprojroot",
    "RSpectra",
    "Rtsne",
    "S7",
    "sass",
    "scales",
    "scattermore",
    "sctransform",
    "Seurat",
    "SeuratObject",
    "shape",
    "shiny",
    "sitmo",
    "sourcetools",
    "sp",
    "spam",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tensor",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "uwot",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "yaml",
    "zoo"
  ],
  "_sysdeps": [
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "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": "algorithm-principles.Rmd",
      "filename": "algorithm-principles.html",
      "title": "Algorithm Principles",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Gene Regulatory Network (GRN) Inference",
        "1.1 Mathematical Formulation",
        "1.2 Ridge Regression",
        "1.3 Bootstrap Aggregation (Bagging)",
        "2. Signal Propagation Simulation",
        "2.1 Perturbation Model",
        "2.2 Iterative Propagation",
        "2.3 Non-negativity Constraint",
        "3. Transition Probability Estimation",
        "3.1 Correlation-Based Approach",
        "3.2 Probability Conversion",
        "3.3 Embedding Shift Calculation",
        "4. Markov Chain Simulation",
        "4.1 State Transition Model",
        "4.2 Trajectory Simulation",
        "4.3 Fate Probability",
        "5. Network Analysis Metrics",
        "5.1 Centrality Measures",
        "5.2 Network Entropy",
        "Summary",
        "References",
        "Session Info"
      ],
      "created": "2026-01-24 17:55:43",
      "modified": "2026-01-24 17:55:43",
      "commits": 1
    },
    {
      "source": "case-study.Rmd",
      "filename": "case-study.html",
      "title": "Case Study: Hematopoiesis",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Biological Background",
        "Hematopoietic Hierarchy",
        "Key Transcription Factors",
        "Simulated Data Setup",
        "Analysis Workflow",
        "Step 1: Create Oracle Object",
        "Step 2: Import Base GRN",
        "Step 3: Fit GRN",
        "Step 4: Simulate Perturbations",
        "Step 5: Analyze Fate Changes",
        "Step 6: Network Analysis",
        "Results Interpretation",
        "GATA1 Knockout",
        "PU.1 Knockout",
        "Key Findings",
        "Code for Full Analysis",
        "Conclusions",
        "References",
        "Session Info"
      ],
      "created": "2026-01-24 17:55:43",
      "modified": "2026-01-24 17:55:43",
      "commits": 1
    },
    {
      "source": "tutorial.Rmd",
      "filename": "tutorial.html",
      "title": "Getting Started with CellOracleR",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Key Features",
        "Workflow Overview",
        "Installation",
        "Load Libraries",
        "Step 1: Prepare Data",
        "Creating Demo Data",
        "Step 2: Create Oracle Object",
        "Step 3: Import Base GRN",
        "Option A: From Motif Analysis (Recommended)",
        "Option B: From Pre-built Database",
        "Option C: Custom Dictionary",
        "Import to Oracle",
        "Step 4: Preprocessing",
        "Step 5: Fit Cluster-Specific GRN",
        "Step 6: Simulate Perturbation",
        "Step 7: Calculate Transition Probabilities",
        "Step 8: Visualize Results",
        "Cluster Overview",
        "Simulation Flow Field",
        "Gene Expression Changes",
        "Step 9: Network Analysis",
        "Top Regulators",
        "Saving and Loading",
        "Advanced: Comparing Multiple Perturbations",
        "Summary",
        "Next Steps",
        "Session Info"
      ],
      "created": "2026-01-24 17:00:27",
      "modified": "2026-01-24 17:55:43",
      "commits": 3
    },
    {
      "source": "grn-inference.Rmd",
      "filename": "grn-inference.html",
      "title": "GRN Inference Details",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Pipeline Architecture",
        "Step 1: Input Data Preparation",
        "Expression Matrix",
        "TF-Target Prior Dictionary",
        "Step 2: Cluster-Specific GRN Fitting",
        "Per-Cluster Fitting",
        "Step 3: Ridge Regression Details",
        "Regularization Parameter (α)",
        "Handling Zero Variance",
        "Step 4: Bootstrap Aggregation",
        "Algorithm",
        "Coefficient Stability Assessment",
        "Step 5: Links Object",
        "Links Data Structure",
        "Performance Considerations",
        "Computational Complexity",
        "Parallelization",
        "C++ Acceleration",
        "Best Practices",
        "1. Data Quality",
        "2. Appropriate Clustering",
        "3. TF-Target Prior Quality",
        "Summary",
        "Session Info"
      ],
      "created": "2026-01-24 17:55:43",
      "modified": "2026-01-24 17:55:43",
      "commits": 1
    },
    {
      "source": "visualization-gallery.Rmd",
      "filename": "visualization-gallery.html",
      "title": "Visualization Gallery",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Cell Embedding Visualizations",
        "Basic Cluster Plot",
        "Gene Expression Overlay",
        "Simulation Flow Visualizations",
        "Quiver Plot (Vector Field)",
        "Streamline Plot",
        "Network Visualizations",
        "Network Graph",
        "Degree Distribution",
        "Network Scores Ranking",
        "Pseudotime Visualizations",
        "Pseudotime on Embedding",
        "Gene Expression along Pseudotime",
        "Comparison Visualizations",
        "Perturbation Comparison",
        "Customization Guide",
        "Color Palettes",
        "Theme Options",
        "Summary",
        "Session Info"
      ],
      "created": "2026-01-24 17:55:43",
      "modified": "2026-01-24 17:55:43",
      "commits": 1
    }
  ],
  "_score": 3.8750612633917,
  "_indexed": true,
  "_nocasepkg": "celloracler",
  "_universes": [
    "zaoqu-liu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-05-25T10:56:13.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "60c989f8c3e938820fa3a89e61c61d68e127269ce1c3b24392fb96039dce68f1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-05-25T10:56:33.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "39cd8d18cf8133f6b0361088792edc7faee405cbb3235ac7085858a98d271af3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-05-25T10:55:59.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "ee09e2a5b219228f9c650196669d4368d1d98b3380d2def90e6d91eb539f534a",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-05-25T10:56:33.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "1dc7a5f852b09878c857eeb61dc6d75fd8ae81c39c9528efd8d2192cfcaac8db",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-05-25T10:54:39.000Z",
      "arch": "aarch64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "e1c127b7e557d086ce0de05e1dd92e9b1c72d868402e3873600b770efbefd500",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-05-25T10:58:01.000Z",
      "arch": "x86_64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "84e7f88ad65e1861acea414b65b1a70385b393769edefd588274e8c77d012043",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-05-25T10:54:01.000Z",
      "arch": "aarch64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "24fbb079b45df60ba57a751e0b94cb9e2e2746dd353ca4216fae46b3059e1195",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-05-25T10:55:10.000Z",
      "arch": "x86_64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "c8cf3119c48651566fcb81b820ad06eb872c3d83e1edf0d8f9bc66506eceda55",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-05-25T10:56:24.000Z",
      "arch": "emscripten",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "408b732f8120463c0771dcf05a5e144280020496e2390ee4ac6fc5ec67382377",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-05-25T10:54:39.000Z",
      "arch": "x86_64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "e8d2c7dd048c919afeb5ee36fc13f9a9f170253bed05dcc6f8e3ac696e9f8776",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-05-25T10:54:36.000Z",
      "arch": "x86_64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "fb7eac632e8f7427429230bbd7e228edff5cfe348ea6f4a7567cd02ec2bbcc72",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-05-25T10:54:45.000Z",
      "arch": "x86_64",
      "commit": "e60a1b9d84a1b89c2e8f36efc8ea16065f673b57",
      "fileid": "e24f8610af3186894a347f9b108f4ec56b6ab73f19fa8cf1a817c0dc8c22006b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26396474624"
    }
  ]
}