{ "_id": "6a1ad13b1d7bb097a09e1fef", "Package": "flowGraph", "Type": "Package", "Title": "Identifying differential cell populations in flow cytometry data\naccounting for marker frequency", "Version": "1.21.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:54:34 UTC", "RemoteUrl": "https://github.com/bioc/flowGraph", "RemoteRef": "HEAD", "RemoteSha": "04c50272f4094833dc86b890ec0ff147cedf4c31", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:27:17 UTC", "User": "root" }, "Author": "Alice Yue [aut, cre]", "Maintainer": "Alice Yue ", "MD5sum": "d3e2403c3118d6a3f3cf2e38225ce0fc", "_user": "bioc", "_type": "src", "_file": "flowGraph_1.21.0.tar.gz", "_fileid": "2e52b3c9118cc4ed6262a3eea23495c280fedf24ffa44ed1de1387983b18525e", "_filesize": 1762314, "_sha256": "2e52b3c9118cc4ed6262a3eea23495c280fedf24ffa44ed1de1387983b18525e", "_created": "2026-05-30T08:27:17.000Z", "_published": "2026-05-30T11:59:55.568Z", "_jobs": [ { "job": 78636549898, "time": 170, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306839339" }, { "job": 78636549897, "time": 351, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306857138" }, { "job": 78636549896, "time": 311, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306853296" }, { "job": 78636549907, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308008504" }, { "job": 78636549900, "time": 210, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308011800" }, { "job": 78636363682, "time": 222, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306823232" }, { "job": 78636549899, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306835981" }, { "job": 78636549905, "time": 618, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306882524" }, { "job": 78636549901, "time": 562, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306876894" }, { "job": 78636549904, "time": 250, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306846921" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/flowGraph", "_commit": { "id": "04c50272f4094833dc86b890ec0ff147cedf4c31", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380874 }, "_maintainer": { "name": "Alice Yue", "email": "aya43@sfu.ca", "login": "aya49", "description": "", "uuid": 22086811 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "effsize", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "ggiraph", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "visNetwork", "role": "Imports" }, { "package": "htmlwidgets", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "Rdpack", "role": "Imports" }, { "package": "data.table", "version": ">= 1.9.5", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "flowcytometry", "statisticalmethod", "immunooncology", "software", "cellbasedassays", "visualization" ], "_stars": 1, "_contributors": [ { "user": "aya49", "count": 184, "uuid": 22086811 }, { "user": "nturaga", "count": 4, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 342, "source": "https://www.bioconductor.org/packages/stats/bioc/flowGraph" }, "_devurl": "https://github.com/aya49/flowgraph", "_searchresults": 16, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/flowGraph.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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", "title": "Formats time into string.", "topics": [ "tstr" ] } ], "_readme": "https://github.com/bioc/flowGraph/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cli", "codetools", "cpp11", "data.table", "digest", "dplyr", "effsize", "evaluate", "farver", "fastmap", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "fs", "furrr", "future", "gdtools", "generics", "ggiraph", "ggplot2", "ggrepel", "globals", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "igraph", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "listenv", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mime", "parallelly", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "Rdpack", "rlang", "rmarkdown", "S7", "sass", "scales", "stringi", "stringr", "systemfonts", "tibble", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "visNetwork", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "flowGraph.Rmd", "filename": "flowGraph.html", "title": "flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequency", "author": "Alice Yue", "engine": "knitr::rmarkdown", "headings": [ "Installing the package", "Citation", "Introduction", "Cell population naming convention", "Workflow: a simple example", "Data sets contained in the package", "Initializing a flowGraph object", "Input format", "Retrieving results from a flowGraph object", "Accessing and modifying data in a flowGraph object", "Flow cytometry sample meta data", "Feature values", "Feature summary statistics", "Plotting and visualizing results", "Appendix", "Appendix 1: OTher useful plots", "QQ plot", "Boxplot", "Logged p-value vs feature difference", "Customizing the cell hierarchy plot", "Appendix 2: flowGraphSubset, a fast version of the flowGraph constructor", "System information", "References" ], "created": "2020-09-28 20:53:24", "modified": "2021-03-14 23:43:26", "commits": 20 } ], "_score": 4.204119982655925, "_indexed": true, "_nocasepkg": "flowgraph", "_universes": [ "bioc", "aya49" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T08:30:50.000Z", "distro": "noble", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "45ca874e531b29dc96784d027e3fd73833be311fe084c23828b4d43a59ede67e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T08:30:10.000Z", "distro": "noble", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "6a081515c0f76aa84390f691467ab00613025396b10ca8bec8079489107f667d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-30T11:57:28.000Z", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "c8ddb100ee65f2167977e293cca80179fff6a28f485a0661366a8a18a8ac0574", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-30T11:57:41.000Z", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "00bfeb7682350a68f174b8337332f2e562bb5c18c25772dd8fa81220178b3abe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-30T08:29:58.000Z", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "d0c490431f638562a39aadfdb30e7e7dc24149689e330f8d0a1f5efe993ef10b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T08:34:37.000Z", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "58bd53673abe0020982d298ba5d104b88a694404fb146e39466921937f595527", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-30T08:33:55.000Z", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "1b683aa06a911a127acec05341e84c98e07ce3de6ea51af5ad15594539372a9a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T08:28:48.000Z", "commit": "04c50272f4094833dc86b890ec0ff147cedf4c31", "fileid": "9f291017e4a08afeb557f112e29e5db3285fa2cdee869d74ee07df04e7240251", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679155924" } ] }