{
  "_id": "6a168ac2acfb0bcc41d7688e",
  "Package": "multinichenetr",
  "Type": "Package",
  "Title": "MultiNicheNet: a flexible framework for differential cell-cell\ncommunication analysis from multi-sample multi-condition\nsingle-cell transcriptomics data",
  "Version": "2.1.0",
  "Authors@R": "person(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0452-742X\"))",
  "Description": "This package allows you the investigate differences in\nintercellular communication between multiple conditions of\ninterest. It is a flexible framework that enables\nmulti-criteria prioritization of cell-cell communication\npatterns from scRNAseq datasets with complex experimental\ndesigns. These datasets can contain multiple samples (e.g.\npatients) over different groups of interest (e.g. disease\nsubtypes). With MultiNicheNet, you can now better analyze the\ndifferences in cell-cell signaling between the different groups\nof interest.",
  "License": "GPL-3 + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://zaoqu-liu.github.io/multinichenetr/,\nhttps://github.com/Zaoqu-Liu/multinichenetr",
  "BugReports": "https://github.com/Zaoqu-Liu/multinichenetr/issues",
  "LazyData": "yes",
  "LazyDataCompression": "bzip2",
  "biocViews": "",
  "VignetteBuilder": "knitr",
  "Remotes": [
    "github::Zaoqu-Liu/nichenetr"
  ],
  "Additional_repositories": "https://zaoqu-liu.r-universe.dev",
  "RoxygenNote": "7.3.1",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev libglpk-dev libglu1-mesa-dev libgmp3-dev make\nlibgsl0-dev libharfbuzz-dev jags libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibmpfr-dev libopenmpi-dev libssl-dev perl libproj-dev python3\nlibx11-dev zlib1g-dev",
  "Repository": "https://zaoqu-liu.r-universe.dev",
  "Date/Publication": "2026-01-25 04:57:32 UTC",
  "RemoteUrl": "https://github.com/Zaoqu-Liu/multinichenetr",
  "RemoteRef": "main",
  "RemoteSha": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-25 07:21:54 UTC",
    "User": "root"
  },
  "Author": "Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-0452-742X>)",
  "Maintainer": "Zaoqu Liu <liuzaoqu@163.com>",
  "MD5sum": "3b785e28c3375222d3860af781eb7728",
  "_user": "zaoqu-liu",
  "_type": "src",
  "_file": "multinichenetr_2.1.0.tar.gz",
  "_fileid": "5af27c5990fed3fca6512d6768579844459d0116f7a396ede664781b348efd77",
  "_filesize": 17834100,
  "_sha256": "5af27c5990fed3fca6512d6768579844459d0116f7a396ede664781b348efd77",
  "_created": "2026-05-25T07:21:54.000Z",
  "_published": "2026-05-27T06:10:10.047Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78016513291,
      "time": 781,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7193790992"
    },
    {
      "job": 78016513455,
      "time": 756,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7193784351"
    },
    {
      "job": 78016513162,
      "time": 113,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78016513330,
      "time": 496,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7193719377"
    },
    {
      "job": 78016513154,
      "time": 423,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7193596960"
    },
    {
      "job": 78016513549,
      "time": 279,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7193665339"
    },
    {
      "job": 78016513505,
      "time": 675,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7193763127"
    },
    {
      "job": 78016513197,
      "time": 829,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78016513534,
      "time": 751,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7193783329"
    }
  ],
  "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26388436021",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/Zaoqu-Liu/multinichenetr",
  "_commit": {
    "id": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
    "author": "Zaoqu-Liu <liuzaoqu@163.com>",
    "committer": "Zaoqu-Liu <liuzaoqu@163.com>",
    "message": "Fix: Exclude vignettes requiring external Zenodo data\n\n- Only build simple vignettes (quick-start, algorithm-methodology, visualization-gallery)\n- Heavy vignettes requiring external data are pre-rendered in pkgdown docs/\n- Fixes R-universe build failures due to Zenodo connection issues\n",
    "time": 1769317052
  },
  "_maintainer": {
    "name": "Zaoqu Liu",
    "email": "liuzaoqu@163.com",
    "login": "zaoqu-liu",
    "orcid": "0000-0002-0452-742X",
    "description": "AI4S",
    "uuid": 68080738
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "generics",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "muscat",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "scater",
      "role": "Imports"
    },
    {
      "package": "nichenetr",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "locfdr",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "ggbeeswarm",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "tidygraph",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "scran",
      "role": "Imports"
    },
    {
      "package": "UpSetR",
      "role": "Imports"
    },
    {
      "package": "factoextra",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "zaoqu-liu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-04",
      "n": 6
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zaoqu-liu",
      "count": 6,
      "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/multinichenetr"
  },
  "_devurl": "https://github.com/zaoqu-liu/multinichenetr",
  "_pkgdown": "https://zaoqu-liu.github.io/multinichenetr/",
  "_searchresults": 116,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/multinichenetr.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "add_empirical_pval_fdr",
    "add_extra_criterion",
    "alias_to_symbol_SCE",
    "combine_sender_receiver_de",
    "combine_sender_receiver_info_ic",
    "compare_normal_emp_pvals",
    "fix_frq_df",
    "generate_prioritization_tables",
    "generate_prioritization_tables_condition_specific_celltypes_receiver",
    "generate_prioritization_tables_condition_specific_celltypes_sender",
    "generate_prioritization_tables_sampleAgnostic_multifactorial",
    "get_abundance_info",
    "get_avg_pb_exprs",
    "get_DE_info",
    "get_DE_info_sampleAgnostic",
    "get_empirical_pvals",
    "get_FDR_empirical",
    "get_FDR_empirical_plots",
    "get_FDR_empirical_plots_all",
    "get_frac_exprs",
    "get_frac_exprs_sampleAgnostic",
    "get_ligand_activities_targets_DEgenes",
    "get_ligand_activities_targets_DEgenes_beta",
    "get_muscat_exprs_avg",
    "get_muscat_exprs_frac",
    "get_pseudobulk_logCPM_exprs",
    "get_top_n_lr_pairs",
    "infer_intercellular_regulatory_network",
    "lr_target_prior_cor_inference",
    "make_circos_group_comparison",
    "make_circos_one_group",
    "make_DEgene_dotplot_pseudobulk",
    "make_DEgene_dotplot_pseudobulk_batch",
    "make_DEgene_dotplot_pseudobulk_reversed",
    "make_ggraph_ligand_target_links",
    "make_ggraph_signaling_path",
    "make_ligand_activity_plots",
    "make_ligand_activity_target_plot",
    "make_ligand_receptor_violin_plot",
    "make_lite_output",
    "make_lite_output_condition_specific",
    "make_lr_target_correlation_plot",
    "make_lr_target_prior_cor_heatmap",
    "make_lr_target_scatter_plot",
    "make_sample_lr_prod_activity_batch_plots",
    "make_sample_lr_prod_activity_plots",
    "make_sample_lr_prod_activity_plots_Omnipath",
    "make_sample_lr_prod_plots",
    "make_target_violin_plot",
    "makenames_SCE",
    "multi_nichenet_analysis",
    "multi_nichenet_analysis_sampleAgnostic",
    "p.adjust_empirical",
    "perform_muscat_de_analysis",
    "prioritize_condition_specific_receiver",
    "prioritize_condition_specific_sender",
    "process_abund_info",
    "process_abundance_expression_info",
    "process_geneset_data",
    "process_info_to_ic",
    "visualize_network"
  ],
  "_datasets": [
    {
      "name": "geneinfo_alias_human",
      "title": "Gene annotation information: version 2 - january 2022 - suited for alias conversion",
      "object": "geneinfo_alias_human",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "symbol",
        "entrez",
        "alias"
      ],
      "rows": 132328,
      "table": true,
      "tojson": true
    },
    {
      "name": "geneinfo_alias_mouse",
      "title": "Gene annotation information: version 2 - january 2022 - suited for alias conversion",
      "object": "geneinfo_alias_mouse",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "symbol",
        "entrez",
        "alias"
      ],
      "rows": 167942,
      "table": true,
      "tojson": true
    },
    {
      "name": "ligand_target_matrix_test",
      "title": "Ligand-Target Matrix: subset NicheNet 2.0.",
      "object": "ligand_target_matrix_test",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "MMP2",
        "SERPINF1",
        "CD82",
        "GSTP1",
        "B2M",
        "PTGFRN",
        "HLA-C",
        "MSN",
        "PLTP",
        "CD58",
        "DSC3",
        "CIB1",
        "SERPING1",
        "CD99",
        "LAMB3",
        "CALM2",
        "EFEMP1",
        "LUM",
        "LAMC2",
        "ADM",
        "CD47",
        "CLDN1",
        "CFD",
        "TNFSF10",
        "GPI",
        "ECM1",
        "HLA-F",
        "MDK",
        "HSP90B1",
        "GRN",
        "LAMA3",
        "CA12",
        "PAM",
        "DCN",
        "COL1A2",
        "HMGB1",
        "CXCL14",
        "TSPAN3",
        "COPA",
        "PTHLH",
        "EFNA1",
        "CD9",
        "PRNP",
        "RTN4",
        "CD59",
        "BST2",
        "RPS19",
        "S100A10",
        "APP",
        "CXADR",
        "EZR",
        "TIMP1",
        "MFAP2",
        "SAA1",
        "ANXA1",
        "CDH13",
        "LGALS1",
        "CDH1",
        "SPINT1",
        "F11R",
        "COL1A1",
        "ANXA2",
        "LGALS3",
        "IGFBP3",
        "GJB6",
        "IGFBP7",
        "HLA-A",
        "S100A8",
        "PDPN",
        "PSAP",
        "COL17A1",
        "GNAS",
        "ITGB1",
        "IFITM1",
        "SDC4",
        "CTSD",
        "GJB2",
        "SERPINE1",
        "CDCP1",
        "MIF",
        "TGFBI",
        "CD44",
        "GLG1",
        "TIMP3",
        "LGALS3BP",
        "ADAM9",
        "HLA-B",
        "SPARC",
        "S100A9",
        "ITM2B",
        "LTBP1",
        "CDH3",
        "NAMPT",
        "DKK3",
        "ADAM17",
        "CALM1",
        "PLAU",
        "HLA-E",
        "ATP1B1",
        "ARF1",
        "FBLN1",
        "CALR",
        "TNC",
        "LRPAP1"
      ],
      "rows": 1673,
      "table": true,
      "tojson": true
    },
    {
      "name": "sce",
      "title": "SingleCellExperiment object containing scRNAseq data (subsampled)",
      "object": "sce",
      "class": [
        "SingleCellExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "add_empirical_pval_fdr",
      "title": "Add empirical p-values and adjusted p-values to the DE output table.",
      "topics": [
        "add_empirical_pval_fdr"
      ]
    },
    {
      "page": "add_extra_criterion",
      "title": "add_extra_criterion",
      "topics": [
        "add_extra_criterion"
      ]
    },
    {
      "page": "alias_to_symbol_SCE",
      "title": "Convert aliases to official gene symbols in a SingleCellExperiment Object",
      "topics": [
        "alias_to_symbol_SCE"
      ]
    },
    {
      "page": "combine_sender_receiver_de",
      "title": "combine_sender_receiver_de",
      "topics": [
        "combine_sender_receiver_de"
      ]
    },
    {
      "page": "combine_sender_receiver_info_ic",
      "title": "combine_sender_receiver_info_ic",
      "topics": [
        "combine_sender_receiver_info_ic"
      ]
    },
    {
      "page": "compare_normal_emp_pvals",
      "title": "compare_normal_emp_pvals",
      "topics": [
        "compare_normal_emp_pvals"
      ]
    },
    {
      "page": "fix_frq_df",
      "title": "fix_frq_df",
      "topics": [
        "fix_frq_df"
      ]
    },
    {
      "page": "geneinfo_alias_human",
      "title": "Gene annotation information: version 2 - january 2022 - suited for alias conversion",
      "topics": [
        "geneinfo_alias_human"
      ]
    },
    {
      "page": "geneinfo_alias_mouse",
      "title": "Gene annotation information: version 2 - january 2022 - suited for alias conversion",
      "topics": [
        "geneinfo_alias_mouse"
      ]
    },
    {
      "page": "generate_prioritization_tables",
      "title": "generate_prioritization_tables",
      "topics": [
        "generate_prioritization_tables"
      ]
    },
    {
      "page": "generate_prioritization_tables_condition_specific_celltypes_receiver",
      "title": "generate_prioritization_tables_condition_specific_celltypes_receiver",
      "topics": [
        "generate_prioritization_tables_condition_specific_celltypes_receiver"
      ]
    },
    {
      "page": "generate_prioritization_tables_condition_specific_celltypes_sender",
      "title": "generate_prioritization_tables_condition_specific_celltypes_sender",
      "topics": [
        "generate_prioritization_tables_condition_specific_celltypes_sender"
      ]
    },
    {
      "page": "generate_prioritization_tables_sampleAgnostic_multifactorial",
      "title": "generate_prioritization_tables_sampleAgnostic_multifactorial",
      "topics": [
        "generate_prioritization_tables_sampleAgnostic_multifactorial"
      ]
    },
    {
      "page": "get_abundance_info",
      "title": "get_abundance_info",
      "topics": [
        "get_abundance_info"
      ]
    },
    {
      "page": "get_avg_pb_exprs",
      "title": "get_avg_pb_exprs",
      "topics": [
        "get_avg_pb_exprs"
      ]
    },
    {
      "page": "get_DE_info",
      "title": "get_DE_info",
      "topics": [
        "get_DE_info"
      ]
    },
    {
      "page": "get_DE_info_sampleAgnostic",
      "title": "get_DE_info_sampleAgnostic",
      "topics": [
        "get_DE_info_sampleAgnostic"
      ]
    },
    {
      "page": "get_empirical_pvals",
      "title": "get_empirical_pvals",
      "topics": [
        "get_empirical_pvals"
      ]
    },
    {
      "page": "get_FDR_empirical",
      "title": "Add empirical p-values and adjusted p-values to a subset of the DE output table.",
      "topics": [
        "get_FDR_empirical"
      ]
    },
    {
      "page": "get_FDR_empirical_plots",
      "title": "Get diagnostic plots of the empirical null.",
      "topics": [
        "get_FDR_empirical_plots"
      ]
    },
    {
      "page": "get_FDR_empirical_plots_all",
      "title": "Get diagnostic plots of the empirical null.",
      "topics": [
        "get_FDR_empirical_plots_all"
      ]
    },
    {
      "page": "get_frac_exprs",
      "title": "get_frac_exprs",
      "topics": [
        "get_frac_exprs"
      ]
    },
    {
      "page": "get_frac_exprs_sampleAgnostic",
      "title": "get_frac_exprs_sampleAgnostic",
      "topics": [
        "get_frac_exprs_sampleAgnostic"
      ]
    },
    {
      "page": "get_ligand_activities_targets_DEgenes",
      "title": "get_ligand_activities_targets_DEgenes",
      "topics": [
        "get_ligand_activities_targets_DEgenes"
      ]
    },
    {
      "page": "get_ligand_activities_targets_DEgenes_beta",
      "title": "get_ligand_activities_targets_DEgenes_beta",
      "topics": [
        "get_ligand_activities_targets_DEgenes_beta"
      ]
    },
    {
      "page": "get_muscat_exprs_avg",
      "title": "get_muscat_exprs_avg",
      "topics": [
        "get_muscat_exprs_avg"
      ]
    },
    {
      "page": "get_muscat_exprs_frac",
      "title": "get_muscat_exprs_frac",
      "topics": [
        "get_muscat_exprs_frac"
      ]
    },
    {
      "page": "get_pseudobulk_logCPM_exprs",
      "title": "get_pseudobulk_logCPM_exprs",
      "topics": [
        "get_pseudobulk_logCPM_exprs"
      ]
    },
    {
      "page": "get_top_n_lr_pairs",
      "title": "get_top_n_lr_pairs",
      "topics": [
        "get_top_n_lr_pairs"
      ]
    },
    {
      "page": "infer_intercellular_regulatory_network",
      "title": "infer_intercellular_regulatory_network",
      "topics": [
        "infer_intercellular_regulatory_network"
      ]
    },
    {
      "page": "ligand_target_matrix_test",
      "title": "Ligand-Target Matrix: subset NicheNet 2.0.",
      "topics": [
        "ligand_target_matrix_test"
      ]
    },
    {
      "page": "lr_target_prior_cor_inference",
      "title": "lr_target_prior_cor_inference",
      "topics": [
        "lr_target_prior_cor_inference"
      ]
    },
    {
      "page": "make_circos_group_comparison",
      "title": "make_circos_group_comparison",
      "topics": [
        "make_circos_group_comparison"
      ]
    },
    {
      "page": "make_circos_one_group",
      "title": "make_circos_one_group",
      "topics": [
        "make_circos_one_group"
      ]
    },
    {
      "page": "make_DEgene_dotplot_pseudobulk",
      "title": "make_DEgene_dotplot_pseudobulk",
      "topics": [
        "make_DEgene_dotplot_pseudobulk"
      ]
    },
    {
      "page": "make_DEgene_dotplot_pseudobulk_batch",
      "title": "make_DEgene_dotplot_pseudobulk_batch",
      "topics": [
        "make_DEgene_dotplot_pseudobulk_batch"
      ]
    },
    {
      "page": "make_DEgene_dotplot_pseudobulk_reversed",
      "title": "make_DEgene_dotplot_pseudobulk_reversed",
      "topics": [
        "make_DEgene_dotplot_pseudobulk_reversed"
      ]
    },
    {
      "page": "make_ggraph_ligand_target_links",
      "title": "make_ggraph_ligand_target_links",
      "topics": [
        "make_ggraph_ligand_target_links"
      ]
    },
    {
      "page": "make_ggraph_signaling_path",
      "title": "make_ggraph_signaling_path",
      "topics": [
        "make_ggraph_signaling_path"
      ]
    },
    {
      "page": "make_ligand_activity_plots",
      "title": "make_ligand_activity_plots",
      "topics": [
        "make_ligand_activity_plots"
      ]
    },
    {
      "page": "make_ligand_activity_target_plot",
      "title": "make_ligand_activity_target_plot",
      "topics": [
        "make_ligand_activity_target_plot"
      ]
    },
    {
      "page": "make_ligand_receptor_violin_plot",
      "title": "make_ligand_receptor_violin_plot",
      "topics": [
        "make_ligand_receptor_violin_plot"
      ]
    },
    {
      "page": "make_lite_output",
      "title": "make_lite_output",
      "topics": [
        "make_lite_output"
      ]
    },
    {
      "page": "make_lite_output_condition_specific",
      "title": "make_lite_output_condition_specific",
      "topics": [
        "make_lite_output_condition_specific"
      ]
    },
    {
      "page": "make_lr_target_correlation_plot",
      "title": "make_lr_target_correlation_plot",
      "topics": [
        "make_lr_target_correlation_plot"
      ]
    },
    {
      "page": "make_lr_target_prior_cor_heatmap",
      "title": "make_lr_target_prior_cor_heatmap",
      "topics": [
        "make_lr_target_prior_cor_heatmap"
      ]
    },
    {
      "page": "make_lr_target_scatter_plot",
      "title": "make_lr_target_scatter_plot",
      "topics": [
        "make_lr_target_scatter_plot"
      ]
    },
    {
      "page": "make_sample_lr_prod_activity_batch_plots",
      "title": "make_sample_lr_prod_activity_batch_plots",
      "topics": [
        "make_sample_lr_prod_activity_batch_plots"
      ]
    },
    {
      "page": "make_sample_lr_prod_activity_plots",
      "title": "make_sample_lr_prod_activity_plots",
      "topics": [
        "make_sample_lr_prod_activity_plots"
      ]
    },
    {
      "page": "make_sample_lr_prod_activity_plots_Omnipath",
      "title": "make_sample_lr_prod_activity_plots_Omnipath",
      "topics": [
        "make_sample_lr_prod_activity_plots_Omnipath"
      ]
    },
    {
      "page": "make_sample_lr_prod_plots",
      "title": "make_sample_lr_prod_plots",
      "topics": [
        "make_sample_lr_prod_plots"
      ]
    },
    {
      "page": "make_target_violin_plot",
      "title": "make_target_violin_plot",
      "topics": [
        "make_target_violin_plot"
      ]
    },
    {
      "page": "makenames_SCE",
      "title": "make.names of all genes in a SingleCellExperiment Object",
      "topics": [
        "makenames_SCE"
      ]
    },
    {
      "page": "multi_nichenet_analysis",
      "title": "multi_nichenet_analysis",
      "topics": [
        "multi_nichenet_analysis"
      ]
    },
    {
      "page": "multi_nichenet_analysis_sampleAgnostic",
      "title": "multi_nichenet_analysis_sampleAgnostic",
      "topics": [
        "multi_nichenet_analysis_sampleAgnostic"
      ]
    },
    {
      "page": "p.adjust_empirical",
      "title": "Get empirical p-values and adjusted p-values.",
      "topics": [
        "p.adjust_empirical"
      ]
    },
    {
      "page": "perform_muscat_de_analysis",
      "title": "perform_muscat_de_analysis",
      "topics": [
        "perform_muscat_de_analysis"
      ]
    },
    {
      "page": "prioritize_condition_specific_receiver",
      "title": "prioritize_condition_specific_receiver",
      "topics": [
        "prioritize_condition_specific_receiver"
      ]
    },
    {
      "page": "prioritize_condition_specific_sender",
      "title": "prioritize_condition_specific_sender",
      "topics": [
        "prioritize_condition_specific_sender"
      ]
    },
    {
      "page": "process_abund_info",
      "title": "process_abund_info",
      "topics": [
        "process_abund_info"
      ]
    },
    {
      "page": "process_abundance_expression_info",
      "title": "process_abundance_expression_info",
      "topics": [
        "process_abundance_expression_info"
      ]
    },
    {
      "page": "process_geneset_data",
      "title": "process_geneset_data",
      "topics": [
        "process_geneset_data"
      ]
    },
    {
      "page": "process_info_to_ic",
      "title": "process_info_to_ic",
      "topics": [
        "process_info_to_ic"
      ]
    },
    {
      "page": "sce",
      "title": "SingleCellExperiment object containing scRNAseq data (subsampled)",
      "topics": [
        "sce"
      ]
    },
    {
      "page": "visualize_network",
      "title": "visualize_network",
      "topics": [
        "visualize_network"
      ]
    }
  ],
  "_readme": "https://github.com/Zaoqu-Liu/multinichenetr/raw/main/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "aod",
    "askpass",
    "assorthead",
    "backports",
    "base64enc",
    "BBmisc",
    "beachmat",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blme",
    "blob",
    "bluster",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "Cairo",
    "callr",
    "car",
    "carData",
    "caret",
    "caTools",
    "cellranger",
    "checkmate",
    "circlize",
    "class",
    "cli",
    "clipr",
    "clock",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "commonmark",
    "ComplexHeatmap",
    "conflicted",
    "corpcor",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "deldir",
    "dendextend",
    "Deriv",
    "diagram",
    "DiagrammeR",
    "DiceKriging",
    "digest",
    "doBy",
    "doParallel",
    "dotCall64",
    "dplyr",
    "dqrng",
    "DT",
    "dtplyr",
    "e1071",
    "edgeR",
    "ellipse",
    "emmeans",
    "emoa",
    "EnvStats",
    "estimability",
    "evaluate",
    "factoextra",
    "FactoMineR",
    "fANCOVA",
    "farver",
    "fastDummies",
    "fastmap",
    "fastmatch",
    "fdrtool",
    "fitdistrplus",
    "flashClust",
    "FNN",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "forcats",
    "foreach",
    "forecast",
    "foreign",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "gargle",
    "gdtools",
    "genefilter",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggbeeswarm",
    "ggforce",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggpubr",
    "ggraph",
    "ggrastr",
    "ggrepel",
    "ggridges",
    "ggsci",
    "ggsignif",
    "glmmTMB",
    "GlobalOptions",
    "globals",
    "glue",
    "goftest",
    "googledrive",
    "googlesheets4",
    "gower",
    "gplots",
    "graphlayouts",
    "gridExtra",
    "gtable",
    "gtools",
    "hardhat",
    "haven",
    "here",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "ica",
    "ids",
    "igraph",
    "ipred",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lava",
    "lazyeval",
    "leaps",
    "lhs",
    "lifecycle",
    "limma",
    "listenv",
    "lme4",
    "lmerTest",
    "lmtest",
    "locfdr",
    "locfit",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "metapod",
    "mgcv",
    "microbenchmark",
    "mime",
    "miniUI",
    "minqa",
    "mlr",
    "mlrMBO",
    "ModelMetrics",
    "modelr",
    "multcompView",
    "muscat",
    "mvtnorm",
    "nichenetr",
    "nlme",
    "nloptr",
    "nnet",
    "nortest",
    "numDeriv",
    "openssl",
    "otel",
    "parallelly",
    "parallelMap",
    "ParamHelpers",
    "patchwork",
    "pbapply",
    "pbkrtest",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polyclip",
    "polynom",
    "prettyunits",
    "pROC",
    "processx",
    "prodlim",
    "progress",
    "progressr",
    "promises",
    "proxy",
    "ps",
    "purrr",
    "quantreg",
    "R6",
    "ragg",
    "randomForest",
    "RANN",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppHNSW",
    "RcppML",
    "RcppProgress",
    "RcppTOML",
    "Rdpack",
    "readr",
    "readxl",
    "recipes",
    "reformulas",
    "remaCor",
    "rematch",
    "rematch2",
    "reprex",
    "reshape2",
    "reticulate",
    "RhpcBLASctl",
    "rjson",
    "rlang",
    "rmarkdown",
    "ROCR",
    "rpart",
    "rprojroot",
    "RSpectra",
    "RSQLite",
    "rstatix",
    "rstudioapi",
    "rsvd",
    "Rtsne",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sandwich",
    "sass",
    "ScaledMatrix",
    "scales",
    "scater",
    "scattermore",
    "scatterplot3d",
    "scran",
    "sctransform",
    "scuttle",
    "selectr",
    "Seqinfo",
    "Seurat",
    "SeuratObject",
    "shadowtext",
    "shape",
    "shiny",
    "SingleCellExperiment",
    "sitmo",
    "smoof",
    "snow",
    "sourcetools",
    "sp",
    "spam",
    "SparseArray",
    "SparseM",
    "sparsevctrs",
    "spatstat.data",
    "spatstat.explore",
    "spatstat.geom",
    "spatstat.random",
    "spatstat.sparse",
    "spatstat.univar",
    "spatstat.utils",
    "SQUAREM",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sva",
    "sys",
    "systemfonts",
    "tensor",
    "textshaping",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tidyverse",
    "timechange",
    "timeDate",
    "tinytex",
    "TMB",
    "tweenr",
    "tzdb",
    "UpSetR",
    "urca",
    "utf8",
    "uuid",
    "uwot",
    "variancePartition",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "visNetwork",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "algorithm-methodology.Rmd",
      "filename": "algorithm-methodology.html",
      "title": "Algorithm & Methodology",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Theoretical Framework",
        "The Cell-Cell Communication Inference Problem",
        "Why Multi-Sample Analysis?",
        "Core Algorithms",
        "1. Pseudobulk Aggregation",
        "2. Differential Expression Analysis",
        "3. NicheNet Ligand Activity Inference",
        "4. Multi-Criteria Prioritization",
        "Biological Scenarios",
        "Mathematical Details",
        "Expression Fraction Calculation",
        "Cell-Type Specificity Score",
        "Prioritization Score Aggregation",
        "Comparison with Other Methods",
        "Performance Considerations",
        "Computational Complexity",
        "Parallelization",
        "References"
      ],
      "created": "2026-01-23 18:32:49",
      "modified": "2026-01-23 18:32:49",
      "commits": 1
    },
    {
      "source": "quick-start.Rmd",
      "filename": "quick-start.html",
      "title": "Quick Start Guide",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Key Features",
        "Installation",
        "From R-Universe (Recommended)",
        "From GitHub",
        "Quick Start Example",
        "Load Required Packages",
        "Load Example Data",
        "Define Analysis Parameters",
        "Load Prior Knowledge Networks",
        "Run MultiNicheNet Analysis",
        "Explore Results",
        "Basic Visualization",
        "Output Structure",
        "Next Steps",
        "Session Info",
        "Citation"
      ],
      "created": "2026-01-23 18:32:49",
      "modified": "2026-01-23 18:32:49",
      "commits": 1
    },
    {
      "source": "visualization-gallery.Rmd",
      "filename": "visualization-gallery.html",
      "title": "Visualization Gallery",
      "author": "Zaoqu Liu",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overview of Visualization Functions",
        "Sample-Level Visualizations",
        "Ligand-Receptor Product Plots",
        "Differential Expression Visualization",
        "Network Visualizations",
        "Circos Plots",
        "Chord Diagrams",
        "Multi-Criteria Bubble Plots",
        "Mushroom Plots",
        "Ligand Activity Visualizations",
        "Activity Heatmaps",
        "Target Gene Visualizations",
        "Target Gene Expression",
        "Summary Statistics",
        "Overview Barplots",
        "Customization Tips",
        "Color Palettes",
        "Export High-Quality Figures",
        "Session Information"
      ],
      "created": "2026-01-23 18:32:49",
      "modified": "2026-01-23 18:32:49",
      "commits": 1
    }
  ],
  "_score": 4.2405492482825995,
  "_indexed": true,
  "_nocasepkg": "multinichenetr",
  "_universes": [
    "zaoqu-liu"
  ],
  "_binaries": [
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-04-25T08:55:50.000Z",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "4bfe8e830e2f6ca85709d6c32c3c5245a8de2ee9af432482d28178ff6196719a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/24927044332"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-04-25T08:55:37.000Z",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "1667d736173cdd0501756a99ffedcf750aa0056181cfd97cf8fd0b7e3f118dbd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/24927044332"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-05-25T07:27:13.000Z",
      "distro": "noble",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "7f6a64f8d56eedef2670d9d06702f101b9845aff865ab573f8007e5525fc9414",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26388436021"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.0",
      "date": "2026-05-25T07:27:02.000Z",
      "distro": "noble",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "257a9145e9f9b2d5ecb94695d3f8d15df6efc448049e5224f65d4110bba55dd7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26388436021"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.0",
      "date": "2026-05-25T07:24:52.000Z",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "a3572a054341b63e4d02dbdce065a4cd8df411b362fcd41001860642e7548ab9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26388436021"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.0",
      "date": "2026-05-25T07:27:32.000Z",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "7396f4710f82dbc0abafcde2346c788a6fb7320ddc20f83eeeab3a2959e432b1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26388436021"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-05-25T07:24:53.000Z",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "f039242a7b74c06228ff26a88464937795bd7ee495ce80b0ff06648fb319d8ae",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26388436021"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.1.0",
      "date": "2026-05-25T07:24:53.000Z",
      "commit": "8f0a5748b8cd2eafbb1ce1dcbf988e4659847f1b",
      "fileid": "f8ca1ad9ef58deec5ff28dd2dd4834e53b0dc340daeb3c715f7ab2c69bca70e4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26388436021"
    }
  ]
}