{ "_id": "6aebae8d9ceaa78f2009f842", "Package": "cellreportR", "Title": "Cell Culture Microscopy Assay Analysis and Reporting", "Version": "0.2.1.9000", "Authors@R": "c(\nperson(\"Raban\", \"Heller\",\nemail = \"raban.heller@charite.de\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-8006-9742\")),\nperson(\"Leila\", \"Schwindling\", role = \"aut\"),\nperson(\"Alexander\", \"Büchner\", role = \"aut\"),\nperson(\"Lucia\", \"Lindenberger\", role = \"aut\"),\nperson(\"Steffen\", \"Müller\", role = \"aut\"),\nperson(\"Michael\", \"Hannemann\", role = \"aut\"),\nperson(\"Gerhard\", \"Achatz\", role = \"aut\"),\nperson(\"Simone\", \"Rothmiller\", role = \"aut\"))", "Description": "Analysis and reporting pipeline for cell culture assays\nread out by microscopy, starting from segmented single-cell\nexports such as those written by 'segmantR', 'CellProfiler' or\n'QuPath'. Recovers the experimental design from the directory\ntree and the file naming convention, resolves acquisitions into\nthe analysis unit of replication, and standardizes every cell\nagainst the control condition of its own batch. Applies\nthreshold and biological quality control gates, then estimates\neffect sizes with confidence intervals at both unit and cell\nlevel so that the cost of treating cells as replicates is\nvisible rather than assumed. Sample sizes for a follow-up study\nare solved from the confidence bound nearer the null instead of\nthe observed point estimate, after Cohen (1988,\nISBN:9780805802832). Figures, machine-readable tables and a\ngenerated file of every quoted number are emitted from the same\nobjects, and an interactive 'shiny' application provides guided\nanalysis and report export.", "License": "MIT + file LICENSE", "URL": "https://github.com/CTTIR/cellreportR,\nhttps://cttir.github.io/cellreportR/", "BugReports": "https://github.com/CTTIR/cellreportR/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.0.0", "Config/Needs/website": "CTTIR/themakR", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libx11-dev\nzlib1g-dev", "Repository": "https://cttir.r-universe.dev", "Date/Publication": "2026-11-04 19:04:12 UTC", "RemoteUrl": "https://github.com/CTTIR/cellreportR", "RemoteRef": "HEAD", "RemoteSha": "885a8753f220936eb98b851dd2272f10da065417", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-04 22:06:17 UTC", "User": "root" }, "Author": "Raban Heller [aut, cre, cph] (ORCID:\n),\nLeila Schwindling [aut],\nAlexander Büchner [aut],\nLucia Lindenberger [aut],\nSteffen Müller [aut],\nMichael Hannemann [aut],\nGerhard Achatz [aut],\nSimone Rothmiller [aut]", "Maintainer": "Raban Heller ", "_user": "cttir", "_type": "src", "_file": "cellreportR_0.2.1.9000.tar.gz", "_fileid": "https://r2.ropensci.org/faa220e8c0747669a6d9e5c7173348073f209b5d3eb941892f56909c1a52dbd8", "_filesize": 2888199, "_sha256": "faa220e8c0747669a6d9e5c7173348073f209b5d3eb941892f56909c1a52dbd8", "_expires": "2027-02-12T22:15:38.000Z", "_created": "2026-11-04T22:06:17.000Z", "_published": "2026-11-04T22:15:40.683Z", "_upstream": "https://github.com/CTTIR/cellreportR", "_status": "success", "_maintainer": { "name": "Raban Heller", "email": "raban.heller@charite.de", "login": "r-heller", "orcid": "0000-0001-8006-9742", "description": "Doctoral researcher at Charité Universitätsmedizin Berlin, Germany. Focus on biomedical research, biostatistics, and data science.", "uuid": 58561665 }, "_jobs": [ { "job": 126897762228, "time": 442, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13367753410" }, { "job": 126897762240, "time": 434, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13366819787" }, { "job": 126897762353, "time": 289, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13368505299" }, { "job": 126897762577, "time": 289, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13366999790" }, { "job": 126895239168, "time": 280, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13366669071" }, { "job": 126897762343, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13367407457" }, { "job": 126897762372, "time": 382, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13366339864" }, { "job": 126897762548, "time": 365, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13366569619" }, { "job": 126897762229, "time": 423, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13368136825" } ], "_buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153", "_commit": { "id": "885a8753f220936eb98b851dd2272f10da065417", "author": "R. Heller <58561665+r-heller@users.noreply.github.com>", "committer": "R. Heller <58561665+r-heller@users.noreply.github.com>", "message": "Resolve the compatible Boost archive on older R\n", "time": 1793819052 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "readxl", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "bslib", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "flowCore", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shinytest2", "role": "Suggests" }, { "package": "shinyWidgets", "role": "Suggests" }, { "package": "sva", "role": "Suggests" }, { "package": "svglite", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "writexl", "role": "Suggests" } ], "_owner": "cttir", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 1 }, { "week": "2026-24", "n": 4 }, { "week": "2026-26", "n": 3 }, { "week": "2026-33", "n": 8 }, { "week": "2026-34", "n": 3 }, { "week": "2026-40", "n": 8 }, { "week": "2026-42", "n": 4 }, { "week": "2026-43", "n": 3 }, { "week": "2026-44", "n": 4 }, { "week": "2026-45", "n": 4 } ], "_tags": [ { "name": "v0.1.0", "date": "2026-05-04" }, { "name": "manuscript-anchor-2026-08-21", "date": "2026-08-13" } ], "_stars": 0, "_contributors": [ { "user": "r-heller", "count": 43, "uuid": 58561665 } ], "_userbio": { "uuid": 275040041, "type": "organization", "name": "CTTIR", "followers": 11, "description": "Computational Trauma and Tissue Injury Research" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cellreportR" }, "_devurl": "https://github.com/cttir/cellreportr", "_pkgdown": "https://cttir.github.io/cellreportR/", "_searchresults": 11, "_rbuild": "4.6.2", "_assets": [ "extra/cellreportR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "cr_apply_gate", "cr_assign_units", "cr_auc", "cr_background_subtract", "cr_balance_cells", "cr_batch_key", "cr_batch_reference", "cr_blocked_effect", "cr_build_experiment", "cr_centroid_overlap", "cr_channels", "cr_classify_result", "cr_column_map", "cr_compare_levels", "cr_compute_metrics", "cr_confusion_matrix", "cr_conservative_effect", "cr_correct_batch", "cr_dataset", "cr_design", "cr_dose_response", "cr_effect_grid", "cr_effect_size", "cr_enumerate", "cr_example_design", "cr_example_experiment", "cr_example_exports", "cr_example_files", "cr_example_path", "cr_example_screen", "cr_exclude_small", "cr_export_plots", "cr_export_report_audit", "cr_export_report_spec", "cr_export_results", "cr_export_tables", "cr_extract_markers", "cr_figure_caption", "cr_figure_size", "cr_filename_grammar", "cr_filter_cells", "cr_finalize_result", "cr_fold_change", "cr_format_interval", "cr_format_number", "cr_format_percent", "cr_format_pvalue", "cr_ic50", "cr_import_report_spec", "cr_interpretation_lookup", "cr_lab_report", "cr_lab_report_from_evidence", "cr_linetype_scale", "cr_linetypes", "cr_logistic", "cr_macro_name", "cr_macros", "cr_macros_from", "cr_marker_rules", "cr_merge_experiments", "cr_merge_rules", "cr_n_cells", "cr_normalize", "cr_palette", "cr_parse_paths", "cr_path_spec", "cr_plot_comparison", "cr_plot_dose_response", "cr_plot_effect_sizes", "cr_plot_estimates", "cr_plot_foldchange", "cr_plot_forest", "cr_plot_heatmap", "cr_plot_histogram", "cr_plot_intensity", "cr_plot_plate", "cr_plot_qc", "cr_plot_qc_gate", "cr_plot_qc_summary", "cr_plot_result_position", "cr_plot_roc", "cr_plot_sample_size", "cr_plot_scatter", "cr_plot_screen", "cr_plot_spatial", "cr_plot_specificity", "cr_plot_style", "cr_plot_timeline", "cr_power", "cr_power_analysis", "cr_power_grid", "cr_print_report_spec", "cr_qc_doublets", "cr_qc_filter", "cr_qc_gate", "cr_qc_gate_impact", "cr_qc_intensity", "cr_qc_manual", "cr_qc_report", "cr_qc_summary", "cr_read_cellprofiler", "cr_read_cells", "cr_read_design", "cr_read_export", "cr_read_exports", "cr_read_qupath", "cr_read_segmantr", "cr_render_lab_report", "cr_render_report", "cr_report", "cr_report_data", "cr_report_display_data", "cr_report_evidence", "cr_report_hash", "cr_report_profile", "cr_report_provenance", "cr_report_qc", "cr_report_qc_from_log", "cr_report_review_app", "cr_report_spec", "cr_report_style", "cr_roc", "cr_rowcol_to_well", "cr_run_app", "cr_save_figure", "cr_save_plot", "cr_scale_colour", "cr_scale_diverging", "cr_scale_fill", "cr_scale_group", "cr_shape_scale", "cr_shapes", "cr_standardize_batch", "cr_summarize_wells", "cr_table_disposition", "cr_table_qc", "cr_tables", "cr_test", "cr_test_all", "cr_theme", "cr_unit_map", "cr_unit_variability", "cr_validate_experiment", "cr_validate_report_evidence", "cr_validate_report_qc", "cr_validate_report_spec", "cr_well_to_rowcol" ], "_help": [ { "page": "cr_apply_gate", "title": "Apply a QC gate to an experiment", "concept": [ "quality control" ], "topics": [ "cr_apply_gate" ] }, { "page": "cr_assign_units", "title": "Assign cells to analysis units", "concept": [ "import" ], "topics": [ "cr_assign_units" ] }, { "page": "cr_auc", "title": "Compute AUC with confidence interval from a 'cr_result'", "topics": [ "cr_auc" ] }, { "page": "cr_background_subtract", "title": "Subtract background from a channel", "concept": [ "normalization functions" ], "topics": [ "cr_background_subtract" ] }, { "page": "cr_balance_cells", "title": "Balance the number of cells per analysis unit", "concept": [ "quality control" ], "topics": [ "cr_balance_cells" ] }, { "page": "cr_batch_key", "title": "Construct a batch key", "concept": [ "batch standardization functions" ], "topics": [ "cr_batch_key" ] }, { "page": "cr_batch_reference", "title": "Per-batch control reference statistics", "concept": [ "batch standardization functions" ], "topics": [ "cr_batch_reference" ] }, { "page": "cr_blocked_effect", "title": "Block-stratified sensitivity fit", "concept": [ "screen statistics" ], "topics": [ "cr_blocked_effect" ] }, { "page": "cr_build_experiment", "title": "Build a 'cr_experiment' object", "concept": [ "constructors" ], "topics": [ "cr_build_experiment" ] }, { "page": "cr_centroid_overlap", "title": "Centroid overlap between two candidate units", "concept": [ "import" ], "topics": [ "cr_centroid_overlap" ] }, { "page": "cr_channels", "title": "List channels in a 'cr_experiment'", "topics": [ "cr_channels" ] }, { "page": "cr_classify_result", "title": "Deterministically classify numeric results using explicit boundaries", "topics": [ "cr_classify_result" ] }, { "page": "cr_column_map", "title": "Declare a column contract for vendor exports", "concept": [ "import" ], "topics": [ "cr_column_map", "print.cr_column_map" ] }, { "page": "cr_compare_levels", "title": "Compare unit-level and cell-level effect estimates", "concept": [ "effect sizes" ], "topics": [ "cr_compare_levels" ] }, { "page": "cr_compute_metrics", "title": "Compute per-unit summary metrics", "concept": [ "quantification" ], "topics": [ "cr_compute_metrics" ] }, { "page": "cr_confusion_matrix", "title": "Confusion matrix for a logistic 'cr_result'", "topics": [ "cr_confusion_matrix" ] }, { "page": "cr_conservative_effect", "title": "Effect size at the confidence bound nearer the null", "concept": [ "power" ], "topics": [ "cr_conservative_effect" ] }, { "page": "cr_correct_batch", "title": "Correct batch effects", "concept": [ "batch standardization functions" ], "topics": [ "cr_correct_batch" ] }, { "page": "cr_dataset", "title": "Build an ingested data set", "concept": [ "constructors" ], "topics": [ "cr_dataset", "print.cr_dataset", "summary.cr_dataset" ] }, { "page": "cr_design", "title": "Build an experimental design object", "concept": [ "constructors" ], "topics": [ "cr_design", "print.cr_design" ] }, { "page": "cr_dose_response", "title": "Fit a dose-response curve", "topics": [ "cr_dose_response" ] }, { "page": "cr_effect_grid", "title": "Effect sizes for a whole grid of contrasts", "concept": [ "effect sizes" ], "topics": [ "cr_effect_grid" ] }, { "page": "cr_effect_size", "title": "Compute effect sizes between two samples", "concept": [ "effect sizes" ], "topics": [ "cr_effect_size" ] }, { "page": "cr_enumerate", "title": "Write a vector out as an English list", "concept": [ "macros" ], "topics": [ "cr_enumerate" ] }, { "page": "cr_example_design", "title": "Generate an example experimental design", "concept": [ "example data" ], "topics": [ "cr_example_design" ] }, { "page": "cr_example_experiment", "title": "Generate a synthetic 'cr_experiment'", "concept": [ "example data" ], "topics": [ "cr_example_experiment" ] }, { "page": "cr_example_exports", "title": "Write a synthetic export tree", "concept": [ "example data" ], "topics": [ "cr_example_exports" ] }, { "page": "cr_example_files", "title": "Write example files in several on-disk formats", "concept": [ "example data" ], "topics": [ "cr_example_files" ] }, { "page": "cr_example_path", "title": "Locate the example files shipped with the package", "concept": [ "example data" ], "topics": [ "cr_example_path" ] }, { "page": "cr_example_screen", "title": "Generate a synthetic multi-compound screen", "concept": [ "example data" ], "topics": [ "cr_example_screen" ] }, { "page": "cr_exclude_small", "title": "Exclude sub-threshold objects with a data-derived cut-off", "concept": [ "quality control" ], "topics": [ "cr_exclude_small" ] }, { "page": "cr_export_plots", "title": "Export plots to PNG, PDF or SVG in batch", "concept": [ "reporting" ], "topics": [ "cr_export_plots" ] }, { "page": "cr_export_report_audit", "title": "Export report audit provenance as JSON", "topics": [ "cr_export_report_audit" ] }, { "page": "cr_export_report_spec", "title": "Export a report specification as versioned JSON", "topics": [ "cr_export_report_spec" ] }, { "page": "cr_export_results", "title": "Export results to CSV, Excel or RDS", "concept": [ "reporting" ], "topics": [ "cr_export_results" ] }, { "page": "cr_export_tables", "title": "Export a set of tables to CSV or Excel", "concept": [ "reporting" ], "topics": [ "cr_export_tables" ] }, { "page": "cr_extract_markers", "title": "Extract file-name markers into typed flags", "concept": [ "import" ], "topics": [ "cr_extract_markers" ] }, { "page": "cr_figure_caption", "title": "Build a descriptive figure caption", "topics": [ "cr_figure_caption" ] }, { "page": "cr_figure_size", "title": "Standard deterministic figure dimensions", "topics": [ "cr_figure_size" ] }, { "page": "cr_filename_grammar", "title": "Declare the token grammar of an export file name", "concept": [ "import" ], "topics": [ "cr_filename_grammar", "print.cr_filename_grammar" ] }, { "page": "cr_filter_cells", "title": "Filter cells in a 'cr_experiment'", "topics": [ "cr_filter_cells" ] }, { "page": "cr_finalize_result", "title": "Apply a caller-selected QC finalization rule", "topics": [ "cr_finalize_result" ] }, { "page": "cr_fold_change", "title": "Compute fold change relative to a control group", "concept": [ "quantification" ], "topics": [ "cr_fold_change" ] }, { "page": "cr_format_interval", "title": "Format an estimate and confidence interval", "topics": [ "cr_format_interval" ] }, { "page": "cr_format_number", "title": "Format a number for a generated document", "concept": [ "macros" ], "topics": [ "cr_format_number" ] }, { "page": "cr_format_percent", "title": "Format proportions as percentages", "topics": [ "cr_format_percent" ] }, { "page": "cr_format_pvalue", "title": "Format p-values without displaying calculated zero", "topics": [ "cr_format_pvalue" ] }, { "page": "cr_ic50", "title": "Extract IC50 / EC50 from a dose-response fit", "topics": [ "cr_ic50" ] }, { "page": "cr_import_report_spec", "title": "Import a versioned report specification from JSON", "topics": [ "cr_import_report_spec" ] }, { "page": "cr_interpretation_lookup", "title": "Look up explicit interpretation text", "topics": [ "cr_interpretation_lookup" ] }, { "page": "cr_lab_report", "title": "Assemble a laboratory report without recalculating analytical values", "topics": [ "cr_lab_report" ] }, { "page": "cr_lab_report_from_evidence", "title": "Assemble a laboratory report with validated, source-bound quoted values", "topics": [ "cr_lab_report_from_evidence" ] }, { "page": "cr_linetypes", "title": "Stable line types for categorical figures", "topics": [ "cr_linetypes" ] }, { "page": "cr_logistic", "title": "Univariate logistic regression of treatment vs. control", "topics": [ "cr_logistic" ] }, { "page": "cr_macro_name", "title": "Build a macro-safe name", "concept": [ "macros" ], "topics": [ "cr_macro_name" ] }, { "page": "cr_macros", "title": "Emit named values as a generated include file", "concept": [ "macros" ], "topics": [ "cr_macros" ] }, { "page": "cr_macros_from", "title": "Derive generated numbers from a report or a results table", "concept": [ "macros" ], "topics": [ "cr_macros_from" ] }, { "page": "cr_marker_rules", "title": "Declare how parenthetical file-name markers are interpreted", "concept": [ "import" ], "topics": [ "cr_marker_rules" ] }, { "page": "cr_merge_experiments", "title": "Merge multiple experiments", "topics": [ "cr_merge_experiments" ] }, { "page": "cr_merge_rules", "title": "Declare how files are merged into analysis units", "concept": [ "import" ], "topics": [ "cr_merge_rules", "print.cr_merge_rules" ] }, { "page": "cr_n_cells", "title": "Count cells in a 'cr_experiment'", "topics": [ "cr_n_cells" ] }, { "page": "cr_normalize", "title": "Normalize intensity data", "concept": [ "normalization functions" ], "topics": [ "cr_normalize" ] }, { "page": "cr_palette", "title": "Colour-vision-safe palette", "concept": [ "plot design" ], "topics": [ "cr_palette" ] }, { "page": "cr_parse_paths", "title": "Parse design facts out of export paths", "concept": [ "import" ], "topics": [ "cr_parse_paths" ] }, { "page": "cr_path_spec", "title": "Bundle a directory and file-name specification", "concept": [ "import" ], "topics": [ "cr_path_spec", "print.cr_path_spec" ] }, { "page": "cr_plot_comparison", "title": "Comparison panel (box, fold change, p-value) for a single result", "concept": [ "visualisation" ], "topics": [ "cr_plot_comparison" ] }, { "page": "cr_plot_dose_response", "title": "Dose-response plot", "concept": [ "visualisation" ], "topics": [ "cr_plot_dose_response" ] }, { "page": "cr_plot_effect_sizes", "title": "Forest plot of effect sizes", "concept": [ "visualisation" ], "topics": [ "cr_plot_effect_sizes" ] }, { "page": "cr_plot_estimates", "title": "Plot estimates and confidence intervals", "topics": [ "cr_plot_estimates" ] }, { "page": "cr_plot_foldchange", "title": "Fold-change forest plot", "concept": [ "visualisation" ], "topics": [ "cr_plot_foldchange" ] }, { "page": "cr_plot_forest", "title": "Forest plot of effect sizes with confidence intervals", "concept": [ "screen figures" ], "topics": [ "cr_plot_forest" ] }, { "page": "cr_plot_heatmap", "title": "Heatmap of channel medians across groups", "concept": [ "visualisation" ], "topics": [ "cr_plot_heatmap" ] }, { "page": "cr_plot_histogram", "title": "Histogram of channel intensity", "concept": [ "visualisation" ], "topics": [ "cr_plot_histogram" ] }, { "page": "cr_plot_intensity", "title": "Intensity distributions by group", "concept": [ "visualisation" ], "topics": [ "cr_plot_intensity" ] }, { "page": "cr_plot_plate", "title": "Plate-layout heatmap", "concept": [ "visualisation" ], "topics": [ "cr_plot_plate" ] }, { "page": "cr_plot_qc", "title": "QC dashboard", "concept": [ "visualisation" ], "topics": [ "cr_plot_qc" ] }, { "page": "cr_plot_qc_gate", "title": "Quality-control gate diagnostic plot", "concept": [ "screen figures" ], "topics": [ "cr_plot_qc_gate" ] }, { "page": "cr_plot_qc_summary", "title": "Compact text-first QC status plot", "topics": [ "cr_plot_qc_summary" ] }, { "page": "cr_plot_result_position", "title": "Plot a value relative to caller-supplied boundaries", "topics": [ "cr_plot_result_position" ] }, { "page": "cr_plot_roc", "title": "ROC curve plot", "concept": [ "visualisation" ], "topics": [ "cr_plot_roc" ] }, { "page": "cr_plot_sample_size", "title": "Sample-size comparison plot", "concept": [ "screen figures" ], "topics": [ "cr_plot_sample_size" ] }, { "page": "cr_plot_scatter", "title": "Biaxial scatter plot of two channels", "concept": [ "visualisation" ], "topics": [ "cr_plot_scatter" ] }, { "page": "cr_plot_screen", "title": "Distribution figure with the unit of replication overlaid", "concept": [ "screen figures" ], "topics": [ "cr_plot_screen" ] }, { "page": "cr_plot_spatial", "title": "Spatial scatter of cells in a well", "concept": [ "visualisation" ], "topics": [ "cr_plot_spatial" ] }, { "page": "cr_plot_specificity", "title": "Specificity control plot", "concept": [ "screen figures" ], "topics": [ "cr_plot_specificity" ] }, { "page": "cr_plot_style", "title": "Construct a reusable plot style", "topics": [ "cr_plot_style" ] }, { "page": "cr_plot_timeline", "title": "Time-course line plot", "concept": [ "visualisation" ], "topics": [ "cr_plot_timeline" ] }, { "page": "cr_power", "title": "Sample size for a future study, sized twice", "concept": [ "power" ], "topics": [ "cr_power" ] }, { "page": "cr_power_analysis", "title": "Simulated power under independent-cell assumptions", "concept": [ "power" ], "topics": [ "cr_power_analysis" ] }, { "page": "cr_power_grid", "title": "Sample sizes for a whole effect grid", "concept": [ "power" ], "topics": [ "cr_power_grid" ] }, { "page": "cr_print_report_spec", "title": "Print a laboratory report specification", "topics": [ "cr_print_report_spec" ] }, { "page": "cr_qc_doublets", "title": "Flag or remove doublets", "concept": [ "quality control" ], "topics": [ "cr_qc_doublets" ] }, { "page": "cr_qc_filter", "title": "Filter cells by morphology", "concept": [ "quality control" ], "topics": [ "cr_qc_filter" ] }, { "page": "cr_qc_gate", "title": "Gate analysis units against their own in-batch control", "concept": [ "quality control" ], "topics": [ "cr_qc_gate" ] }, { "page": "cr_qc_gate_impact", "title": "Quantify the leverage of gate exclusions", "concept": [ "quality control" ], "topics": [ "cr_qc_gate_impact" ] }, { "page": "cr_qc_intensity", "title": "Gate cells by intensity", "concept": [ "quality control" ], "topics": [ "cr_qc_intensity" ] }, { "page": "cr_qc_manual", "title": "Manually exclude wells or cells", "concept": [ "quality control" ], "topics": [ "cr_qc_manual" ] }, { "page": "cr_qc_report", "title": "Report every analysis unit with its QC verdict", "concept": [ "quality control" ], "topics": [ "cr_qc_report" ] }, { "page": "cr_qc_summary", "title": "Summarise QC steps applied to an experiment", "concept": [ "quality control" ], "topics": [ "cr_qc_summary" ] }, { "page": "cr_read_cellprofiler", "title": "Read a CellProfiler object export", "concept": [ "import" ], "topics": [ "cr_read_cellprofiler" ] }, { "page": "cr_read_cells", "title": "Read segmented cell data from file", "concept": [ "import" ], "topics": [ "cr_read_cells" ] }, { "page": "cr_read_design", "title": "Read experimental design from CSV or Excel", "concept": [ "import" ], "topics": [ "cr_read_design" ] }, { "page": "cr_read_export", "title": "Read one segmented single-cell export", "concept": [ "import" ], "topics": [ "cr_read_export" ] }, { "page": "cr_read_exports", "title": "Read a directory tree of segmented single-cell exports", "concept": [ "import" ], "topics": [ "cr_read_exports" ] }, { "page": "cr_read_qupath", "title": "Read a QuPath measurement export", "concept": [ "import" ], "topics": [ "cr_read_qupath" ] }, { "page": "cr_read_segmantr", "title": "Read a segmantR result", "concept": [ "import" ], "topics": [ "cr_read_segmantr" ] }, { "page": "cr_render_lab_report", "title": "Render a concise laboratory report", "topics": [ "cr_render_lab_report" ] }, { "page": "cr_render_report", "title": "Render a report to HTML or PDF", "concept": [ "reporting" ], "topics": [ "cr_render_report" ] }, { "page": "cr_report", "title": "Assemble a structured analysis report", "concept": [ "reporting" ], "topics": [ "cr_report" ] }, { "page": "cr_report_data", "title": "Inspect the exact structured values entering a laboratory report", "topics": [ "cr_report_data" ] }, { "page": "cr_report_display_data", "title": "Prepare human-facing values for report rendering", "concept": [ "laboratory reporting" ], "topics": [ "cr_report_display_data" ] }, { "page": "cr_report_evidence", "title": "Bind report claims and figures to portable source-file evidence", "topics": [ "cr_report_evidence" ] }, { "page": "cr_report_hash", "title": "Hash report-relevant structured data", "topics": [ "cr_report_hash" ] }, { "page": "cr_report_profile", "title": "Create a reusable laboratory report profile", "concept": [ "laboratory reporting" ], "topics": [ "cr_report_profile" ] }, { "page": "cr_report_provenance", "title": "Build machine-readable report provenance", "topics": [ "cr_report_provenance" ] }, { "page": "cr_report_qc", "title": "Construct a concise report QC table", "topics": [ "cr_report_qc" ] }, { "page": "cr_report_qc_from_log", "title": "Convert an existing experiment QC log to report-compatible rows", "topics": [ "cr_report_qc_from_log" ] }, { "page": "cr_report_review_app", "title": "Review an immutable source-bound report in a Shiny application", "topics": [ "cr_report_review_app" ] }, { "page": "cr_report_spec", "title": "Construct a configurable laboratory report specification", "concept": [ "laboratory reporting" ], "topics": [ "cr_report_spec" ] }, { "page": "cr_report_style", "title": "Configure the appearance of laboratory reports", "concept": [ "laboratory reporting" ], "topics": [ "cr_report_style" ] }, { "page": "cr_roc", "title": "Extract or compute an ROC curve from a 'cr_result'", "topics": [ "cr_roc" ] }, { "page": "cr_rowcol_to_well", "title": "Convert row and column indices to well IDs", "topics": [ "cr_rowcol_to_well" ] }, { "page": "cr_run_app", "title": "Launch the cellreportR Shiny application", "concept": [ "cellreportR-app" ], "topics": [ "cr_run_app" ] }, { "page": "cr_save_figure", "title": "Save a publication-ready figure deterministically", "topics": [ "cr_save_figure" ] }, { "page": "cr_save_plot", "title": "Save a figure at publication settings", "concept": [ "screen figures" ], "topics": [ "cr_save_plot" ] }, { "page": "cr_scale_colour", "title": "Manual colour scale from the cellreportR visual system", "topics": [ "cr_linetype_scale", "cr_scale_colour", "cr_scale_fill", "cr_shape_scale" ] }, { "page": "cr_scale_diverging", "title": "Continuous diverging scale", "topics": [ "cr_scale_diverging" ] }, { "page": "cr_scale_group", "title": "Grouping scales with redundant encoding", "concept": [ "plot design" ], "topics": [ "cr_scale_group" ] }, { "page": "cr_shapes", "title": "Redundant shape encoding", "concept": [ "plot design" ], "topics": [ "cr_shapes" ] }, { "page": "cr_standardize_batch", "title": "Standardize a channel against the control of each cell's own batch", "concept": [ "batch standardization functions" ], "topics": [ "cr_standardize_batch" ] }, { "page": "cr_summarize_wells", "title": "Summarize cell-level data to the analysis unit", "concept": [ "quantification" ], "topics": [ "cr_summarize_wells" ] }, { "page": "cr_table_disposition", "title": "Tabulate how many units and cells entered the analysis", "concept": [ "quantification" ], "topics": [ "cr_table_disposition" ] }, { "page": "cr_table_qc", "title": "Tabulate the quality-control record", "concept": [ "reporting" ], "topics": [ "cr_table_qc" ] }, { "page": "cr_tables", "title": "Collect the tables of an analysis", "concept": [ "reporting" ], "topics": [ "cr_tables" ] }, { "page": "cr_test", "title": "Hypothesis test comparing treatment to control", "concept": [ "statistics" ], "topics": [ "cr_test" ] }, { "page": "cr_test_all", "title": "Test all treatments against a control group", "concept": [ "statistics" ], "topics": [ "cr_test_all" ] }, { "page": "cr_theme", "title": "Publication theme", "concept": [ "plot design" ], "topics": [ "cr_theme" ] }, { "page": "cr_unit_map", "title": "Map source files to analysis units", "concept": [ "import" ], "topics": [ "cr_unit_map" ] }, { "page": "cr_unit_variability", "title": "Between-unit variability within a condition", "concept": [ "screen statistics" ], "topics": [ "cr_unit_variability" ] }, { "page": "cr_validate_experiment", "title": "Validate a 'cr_experiment'", "concept": [ "constructors" ], "topics": [ "cr_validate_experiment" ] }, { "page": "cr_validate_report_evidence", "title": "Revalidate report evidence against its current source tree", "topics": [ "cr_validate_report_evidence" ] }, { "page": "cr_validate_report_qc", "title": "Validate a concise report QC table", "topics": [ "cr_validate_report_qc" ] }, { "page": "cr_validate_report_spec", "title": "Validate a laboratory report specification", "concept": [ "laboratory reporting" ], "topics": [ "cr_validate_report_spec" ] }, { "page": "cr_well_to_rowcol", "title": "Convert well IDs to row and column indices", "topics": [ "cr_well_to_rowcol" ] }, { "page": "print.cr_experiment", "title": "Print method for 'cr_experiment'", "topics": [ "print.cr_experiment" ] }, { "page": "print.cr_qc_gate", "title": "Print a QC gate", "concept": [ "quality control" ], "topics": [ "print.cr_qc_gate" ] }, { "page": "print.cr_report", "title": "Print method for 'cr_report'", "topics": [ "print.cr_report" ] }, { "page": "print.cr_result", "title": "Print method for 'cr_result'", "topics": [ "print.cr_result" ] }, { "page": "summary.cr_experiment", "title": "Summary method for 'cr_experiment'", "topics": [ "summary.cr_experiment" ] }, { "page": "summary.cr_report", "title": "Summary method for 'cr_report'", "topics": [ "summary.cr_report" ] }, { "page": "summary.cr_result", "title": "Summary method for 'cr_result'", "topics": [ "summary.cr_result" ] } ], "_pkglogo": "https://github.com/CTTIR/cellreportR/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/CTTIR/cellreportR/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bit", "bit64", "bslib", "cachem", "cellranger", "cli", "clipr", "commonmark", "cpp11", "crayon", "digest", "dplyr", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gtable", "hms", "htmltools", "httpuv", "isoband", "jquerylib", "jsonlite", "labeling", "later", "lifecycle", "magrittr", "memoise", "mime", "otel", "pillar", "pkgconfig", "prettyunits", "pROC", "progress", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "readr", "readxl", "rematch", "rlang", "S7", "sass", "scales", "shiny", "sourcetools", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "xtable" ], "_vignettes": [ { "source": "laboratory-reporting.Rmd", "filename": "laboratory-reporting.html", "title": "Configurable Laboratory Reports with cellreportR", "engine": "knitr::rmarkdown", "headings": [ "Report design and document control" ], "created": "2026-08-13 12:48:06", "modified": "2026-10-28 07:28:55", "commits": 4 }, { "source": "dose-response.Rmd", "filename": "dose-response.html", "title": "Dose-Response Analysis", "engine": "knitr::rmarkdown", "headings": [ "Setting up an exposure axis", "Fitting", "IC50 / EC50", "Plotting", "Comparing models", "Checking that the fit converged", "Where this fits" ], "created": "2026-05-04 17:52:01", "modified": "2026-10-28 07:28:55", "commits": 5 }, { "source": "end-to-end.Rmd", "filename": "end-to-end.html", "title": "End to End: From Segmented Exports to a Finished Report", "engine": "knitr::rmarkdown", "headings": [ "1. Ingest: the design lives in the tree and the file name", "Column names, path levels, file-name grammar", "Files are not units", "2. Scaling up", "3. Quality control at the cell level", "4. Standardization against each unit's own control", "5. The unit-level gate, and what it costs", "6. Effect sizes at both levels", "7. Sample size for the follow-up study", "8. The report", "What was decided, and where it is recorded", "Next steps" ], "created": "2026-08-13 11:20:05", "modified": "2026-10-28 07:28:55", "commits": 3 }, { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting Started with cellreportR", "engine": "knitr::rmarkdown", "headings": [ "1. Load example data", "2. Inspect the design", "3. Apply quality control", "4. Fold changes and tests", "5. Visualize", "6. Discriminability", "7. Next steps" ], "created": "2026-05-04 17:52:01", "modified": "2026-10-28 07:28:55", "commits": 7 }, { "source": "shiny-app.Rmd", "filename": "shiny-app.html", "title": "Interactive Analysis with the cellreportR Shiny App", "engine": "knitr::rmarkdown", "headings": [ "Launching", "Layout", "The sidebar", "The tabs", "Cross-tab state", "Deployment" ], "created": "2026-05-04 17:52:01", "modified": "2026-10-30 10:15:50", "commits": 6 }, { "source": "figure-style.Rmd", "filename": "figure-style.html", "title": "Publication-ready figures with cellreportR", "engine": "knitr::rmarkdown", "headings": [], "created": "2026-08-13 12:48:06", "modified": "2026-10-28 07:28:55", "commits": 2 }, { "source": "statistical-analysis.Rmd", "filename": "statistical-analysis.html", "title": "Statistical Analysis of Cell-Based Assays", "engine": "knitr::rmarkdown", "headings": [ "Why the level of aggregation matters", "A worked example", "Effect size interpretation", "ROC and AUC for discriminability", "Multiple testing", "Power and sample size", "Where this fits" ], "created": "2026-05-04 17:52:01", "modified": "2026-10-30 10:15:50", "commits": 6 } ], "_score": 4.585460729508501, "_indexed": true, "_nocasepkg": "cellreportr", "_universes": [ "cttir", "r-heller" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.1.9000", "date": "2026-11-04T22:09:32.000Z", "distro": "resolute", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/c1011c50e73a3fd9c2bcf6bf04e65a8fc570aa0cecc4689b75e675a5f1dfc836", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" }, { "r": "4.6.2", "os": "linux", "version": "0.2.1.9000", "date": "2026-11-04T22:09:23.000Z", "distro": "resolute", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/58b3bf6b867c8be8490a7a5e8d052e73a455742ad251e1967d70ae4dafcad093", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" }, { "r": "4.5.3", "os": "mac", "version": "0.2.1.9000", "date": "2026-11-04T22:09:11.000Z", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/9ee065e463598e6f8c3c44b93120ebc0d130a7691e32120287e3b9e54f36c252", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" }, { "r": "4.6.2", "os": "mac", "version": "0.2.1.9000", "date": "2026-11-04T22:09:27.000Z", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/a482870229e810b7a299c2629a121642d9c4cd6562874235d46ac157c9dd27aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.1.9000", "date": "2026-11-04T22:09:25.000Z", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/38eff37b306e850bb66b581324cff9f019ba6ef409529e0f61500313227d0f47", "status": "success", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" }, { "r": "4.7.0", "os": "win", "version": "0.2.1.9000", "date": "2026-11-04T22:08:32.000Z", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/4d912a3b51945e68eb0e40bcaa94f79d0757f19143bca4a394b1788255ee5368", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" }, { "r": "4.5.3", "os": "win", "version": "0.2.1.9000", "date": "2026-11-04T22:08:15.000Z", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/94edf500cb3484715af7cba074161636bdae050b146673c25731c239c81e3d48", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" }, { "r": "4.6.2", "os": "win", "version": "0.2.1.9000", "date": "2026-11-04T22:08:16.000Z", "commit": "885a8753f220936eb98b851dd2272f10da065417", "fileid": "https://r2.ropensci.org/29a2879ab098bef620c89614d237d33f9240efbac401a056ed92856b99f05312", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cttir/actions/runs/41921558153" } ] }