{
  "_id": "6a195927acfb0bcc41de3796",
  "Package": "flowGraph",
  "Type": "Package",
  "Title": "Identifying differential cell populations in flow cytometry data\naccounting for marker frequency",
  "Version": "1.20.0",
  "Description": "Identifies maximal differential cell populations in flow\ncytometry data taking into account dependencies between cell\npopulations; flowGraph calculates and plots SpecEnr abundance\nscores given cell population cell counts.",
  "Date": "2019-11-30",
  "Authors@R": "person(\"Alice\", \"Yue\", email = \"aya43@sfu.ca\", role = c(\"aut\", \"cre\"))",
  "License": "Artistic-2.0",
  "VignetteBuilder": "knitr",
  "biocViews": "FlowCytometry, StatisticalMethod, ImmunoOncology, Software,\nCellBasedAssays, Visualization",
  "BugReports": "https://github.com/aya49/flowGraph/issues",
  "URL": "https://github.com/aya49/flowGraph",
  "RoxygenNote": "7.1.1",
  "RdMacros": "Rdpack",
  "LazyData": "no",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:34 UTC",
  "RemoteUrl": "https://github.com/bioc/flowGraph",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "18c93d78709bf69d13c7ecd20571ba220b7095b9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 07:55:16 UTC",
    "User": "root"
  },
  "Author": "Alice Yue [aut, cre]",
  "Maintainer": "Alice Yue <aya43@sfu.ca>",
  "MD5sum": "4885df0b8b5f47ecc5337efac67531d1",
  "_user": "bioc-release",
  "_type": "src",
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  "_created": "2026-05-29T07:55:16.000Z",
  "_published": "2026-05-29T09:15:19.066Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
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    },
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    "statisticalmethod",
    "immunooncology",
    "software",
    "cellbasedassays",
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  ],
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  "_contributors": [
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
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    "count": 342,
    "source": "https://www.bioconductor.org/packages/stats/bioc/flowGraph"
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  "_devurl": "https://github.com/aya49/flowgraph",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/readme.md",
    "manual.pdf"
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  "_homeurl": "https://github.com/aya49/flowgraph",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cell_type_layers",
    "fg_add_feature",
    "fg_add_summary",
    "fg_clear_features",
    "fg_clear_summary",
    "fg_extract_phenotypes",
    "fg_extract_raw",
    "fg_extract_samples",
    "fg_feat_edge_prop",
    "fg_feat_edge_specenr",
    "fg_feat_mean_class",
    "fg_feat_node_prop",
    "fg_feat_node_specenr",
    "fg_get_feature",
    "fg_get_feature_desc",
    "fg_get_feature_means",
    "fg_get_graph",
    "fg_get_markers",
    "fg_get_meta",
    "fg_get_summary",
    "fg_get_summary_desc",
    "fg_get_summary_index",
    "fg_get_summary_tables",
    "fg_gsub_ids",
    "fg_gsub_markers",
    "fg_load",
    "fg_merge",
    "fg_merge_samples",
    "fg_plot",
    "fg_plot_box",
    "fg_plot_pVSdiff",
    "fg_plot_qq",
    "fg_replace_meta",
    "fg_rm_feature",
    "fg_rm_summary",
    "fg_save",
    "fg_save_plots",
    "fg_set_layout",
    "fg_summary",
    "flowGraph",
    "flowGraphSubset",
    "flowGraphSubset_summary_adjust",
    "flowGraphSubset_summary_pars",
    "get_phen_list",
    "get_phen_meta",
    "ggdf",
    "plot_gr",
    "set_layout_graph",
    "show",
    "summary_table"
  ],
  "_datasets": [
    {
      "name": "fg_data_fca",
      "title": "fg_data_fca",
      "object": "fg_data_fca",
      "file": "fg_data_fca.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "fg_data_pos2",
      "title": "fg_data_pos2",
      "object": "fg_data_pos2",
      "file": "fg_data_pos2.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "fg_data_pos30",
      "title": "fg_data_pos30",
      "object": "fg_data_pos30",
      "file": "fg_data_pos30.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "cell_type_layers",
      "title": "Determines the layer on which a phenotype resides.",
      "topics": [
        "cell_type_layers"
      ]
    },
    {
      "page": "extract_markers",
      "title": "Extracts markers from cell population phenotypes",
      "topics": [
        "extract_markers"
      ]
    },
    {
      "page": "fg_add_feature",
      "title": "Adds a feature.",
      "topics": [
        "fg_add_feature"
      ]
    },
    {
      "page": "fg_add_summary",
      "title": "Adds a feature summary.",
      "topics": [
        "fg_add_summary"
      ]
    },
    {
      "page": "fg_clean_phen",
      "title": "Reformats phenotype",
      "topics": [
        "fg_clean_phen"
      ]
    },
    {
      "page": "fg_clear_features",
      "title": "Clears all featuresin a flowGraph object.",
      "topics": [
        "fg_clear_features"
      ]
    },
    {
      "page": "fg_clear_summary",
      "title": "Removes all summary statistics.",
      "topics": [
        "fg_clear_summary"
      ]
    },
    {
      "page": "fg_data_fca",
      "title": "fg_data_fca",
      "topics": [
        "fg_data_fca"
      ]
    },
    {
      "page": "fg_data_pos2",
      "title": "fg_data_pos2",
      "topics": [
        "fg_data_pos2"
      ]
    },
    {
      "page": "fg_data_pos30",
      "title": "fg_data_pos30",
      "topics": [
        "fg_data_pos30"
      ]
    },
    {
      "page": "fg_extract_phenotypes",
      "title": "Extracts a set of phenotypes from a flowGraph object.",
      "topics": [
        "fg_extract_phenotypes"
      ]
    },
    {
      "page": "fg_extract_raw",
      "title": "Clears all features and feature summaries in a flowGraph object.",
      "topics": [
        "fg_extract_raw"
      ]
    },
    {
      "page": "fg_extract_samples",
      "title": "Extracts a set of samples from a flowGraph object.",
      "topics": [
        "fg_extract_samples"
      ]
    },
    {
      "page": "fg_feat_cumsum",
      "title": "Converts cell counts into cumulated cell counts.",
      "topics": [
        "fg_feat_cumsum"
      ]
    },
    {
      "page": "fg_feat_prop_edge",
      "title": "Generates the proportion edge feature.",
      "topics": [
        "fg_feat_edge_prop"
      ]
    },
    {
      "page": "fg_feat_edge_specenr",
      "title": "Generates the SpecEnr edge feature.",
      "topics": [
        "fg_feat_edge_specenr"
      ]
    },
    {
      "page": "fg_feat_mean_class",
      "title": "Normalizes all features for class.",
      "topics": [
        "fg_feat_mean_class"
      ]
    },
    {
      "page": "fg_feat_node_prop",
      "title": "Generates the proportion node feature.",
      "topics": [
        "fg_feat_node_prop"
      ]
    },
    {
      "page": "fg_feat_node_specenr",
      "title": "Generates the SpecEnr node feature.",
      "topics": [
        "fg_feat_node_specenr"
      ]
    },
    {
      "page": "fg_get_feature",
      "title": "Retrieves a feature matrix.",
      "topics": [
        "fg_get_feature"
      ]
    },
    {
      "page": "fg_get_feature_desc",
      "title": "Retrieves and/or recalculates a feature description table.",
      "topics": [
        "fg_get_feature_desc"
      ]
    },
    {
      "page": "fg_get_feature_means",
      "title": "Retrieves feature summaries.",
      "topics": [
        "fg_get_feature_means"
      ]
    },
    {
      "page": "fg_get_graph",
      "title": "Retrieves a graph list from a given flowGraph object.",
      "topics": [
        "fg_get_graph"
      ]
    },
    {
      "page": "fg_get_markers",
      "title": "Retrieves the markers from a given flowGraph object.",
      "topics": [
        "fg_get_markers"
      ]
    },
    {
      "page": "fg_get_meta",
      "title": "Retrieves sample meta.",
      "topics": [
        "fg_get_meta"
      ]
    },
    {
      "page": "fg_get_summary",
      "title": "Retrieves a summary statistic.",
      "topics": [
        "fg_get_summary"
      ]
    },
    {
      "page": "fg_get_summary_desc",
      "title": "Retrieves a feature summary description table.",
      "topics": [
        "fg_get_summary_desc"
      ]
    },
    {
      "page": "fg_get_summary_index",
      "title": "Retrieves the index of the requested summary.",
      "topics": [
        "fg_get_summary_index"
      ]
    },
    {
      "page": "fg_get_summary_tables",
      "title": "Retrieves a table containing all node or edge summary statistics.",
      "topics": [
        "fg_get_summary_tables"
      ]
    },
    {
      "page": "fg_gsub_ids",
      "title": "Replace sample id's.",
      "topics": [
        "fg_gsub_ids"
      ]
    },
    {
      "page": "fg_gsub_markers",
      "title": "Replace marker names.",
      "topics": [
        "fg_gsub_markers"
      ]
    },
    {
      "page": "fg_load",
      "title": "Load a flowGraph object from a specified folder path.",
      "topics": [
        "fg_load"
      ]
    },
    {
      "page": "fg_merge",
      "title": "Merges two flowGraph objects together.",
      "topics": [
        "fg_merge"
      ]
    },
    {
      "page": "fg_merge_samples",
      "title": "Merges the samples from two flowGraph objects.",
      "topics": [
        "fg_merge_samples"
      ]
    },
    {
      "page": "fg_plot",
      "title": "Creates a cell hierarchy plot.",
      "topics": [
        "fg_plot"
      ]
    },
    {
      "page": "fg_plot_box",
      "title": "Creates a boxplot of the values of one node/edge",
      "topics": [
        "fg_plot_box"
      ]
    },
    {
      "page": "fg_plot_pVSdiff",
      "title": "Creates a p value vs feature difference plot",
      "topics": [
        "fg_plot_pVSdiff"
      ]
    },
    {
      "page": "fg_plot_qq",
      "title": "Creates a QQ plot of a summary statistic.",
      "topics": [
        "fg_plot_qq"
      ]
    },
    {
      "page": "fg_replace_meta",
      "title": "Replaces sample meta.",
      "topics": [
        "fg_replace_meta"
      ]
    },
    {
      "page": "fg_rm_feature",
      "title": "Removes a feature.",
      "topics": [
        "fg_rm_feature"
      ]
    },
    {
      "page": "fg_rm_summary",
      "title": "Removes a feature summary.",
      "topics": [
        "fg_rm_summary"
      ]
    },
    {
      "page": "fg_save",
      "title": "Saves flowGraph object to a specified path.",
      "topics": [
        "fg_save"
      ]
    },
    {
      "page": "fg_save_plots",
      "title": "Saves numerous plots for all summary statistics to a folder.",
      "topics": [
        "fg_save_plots"
      ]
    },
    {
      "page": "fg_set_layout",
      "title": "Determines cell hierarchy layout.",
      "topics": [
        "fg_set_layout"
      ]
    },
    {
      "page": "fg_summary",
      "title": "Calculates feature summary statistics.",
      "topics": [
        "fg_summary"
      ]
    },
    {
      "page": "flowGraph",
      "title": "flowGraph object constructor.",
      "topics": [
        "flowGraph"
      ]
    },
    {
      "page": "flowGraph-class",
      "title": "'flowGraph': A class for storing cell count feature values for the Phenotype class.",
      "topics": [
        "flowGraph-class",
        "show,flowGraph-method"
      ]
    },
    {
      "page": "flowGraphSubset",
      "title": "flowGraph object constructor.",
      "topics": [
        "flowGraphSubset"
      ]
    },
    {
      "page": "flowGraphSubset_summary_adjust",
      "title": "Default for flowGraphSubset's summary_adjust",
      "topics": [
        "flowGraphSubset_summary_adjust"
      ]
    },
    {
      "page": "flowGraphSubset_summary_pars",
      "title": "Default for flowGraphSubset's summary_pars",
      "topics": [
        "flowGraphSubset_summary_pars"
      ]
    },
    {
      "page": "fpurrr_map",
      "title": "Wrapper for map",
      "topics": [
        "fpurrr_map"
      ]
    },
    {
      "page": "get_child",
      "title": "Gets child populations of given cell populations",
      "topics": [
        "get_child"
      ]
    },
    {
      "page": "get_eprop",
      "title": "Gets edge proportions of a given edge matrix",
      "topics": [
        "get_eprop"
      ]
    },
    {
      "page": "get_paren",
      "title": "Gets parent populations of given cell populations",
      "topics": [
        "get_paren"
      ]
    },
    {
      "page": "get_phen_list",
      "title": "Creates edge lists.",
      "topics": [
        "get_phen_list"
      ]
    },
    {
      "page": "get_phen_meta",
      "title": "Genrates phenotype meta data.",
      "topics": [
        "get_phen_meta"
      ]
    },
    {
      "page": "ggdf",
      "title": "Prepares a given node and edge graph list for plotting.",
      "topics": [
        "ggdf"
      ]
    },
    {
      "page": "loop_ind_f",
      "title": "Prepares parallel loop indices.",
      "topics": [
        "loop_ind_f"
      ]
    },
    {
      "page": "meandiff",
      "title": "Normalizes matrix values by class.",
      "topics": [
        "mean_diff"
      ]
    },
    {
      "page": "ms_create",
      "title": "Calcuate SpecEnr from proportion and expected proportion",
      "topics": [
        "ms_create"
      ]
    },
    {
      "page": "ms_psig",
      "title": "Determines which phenotypes are statistically significant",
      "topics": [
        "ms_psig"
      ]
    },
    {
      "page": "plot_gr",
      "title": "Plots a cell hierarchy.",
      "topics": [
        "plot_gr"
      ]
    },
    {
      "page": "set_layout_graph",
      "title": "Determines cell hierarchy layout.",
      "topics": [
        "set_layout_graph"
      ]
    },
    {
      "page": "summary_table",
      "title": "Summarizes a numeric matrix.",
      "topics": [
        "summary_table"
      ]
    },
    {
      "page": "test_c",
      "title": "Converts input into a significance test function",
      "topics": [
        "test_c"
      ]
    },
    {
      "page": "time_output",
      "title": "Outputs elapsed time.",
      "topics": [
        "time_output"
      ]
    },
    {
      "page": "tstr",
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        "Citation",
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