Package: cellreportR 0.2.1.9000

Raban Heller

cellreportR: Cell Culture Microscopy Assay Analysis and Reporting

Analysis and reporting pipeline for cell culture assays read out by microscopy, starting from segmented single-cell exports such as those written by 'segmantR', 'CellProfiler' or 'QuPath'. Recovers the experimental design from the directory tree and the file naming convention, resolves acquisitions into the analysis unit of replication, and standardizes every cell against the control condition of its own batch. Applies threshold and biological quality control gates, then estimates effect sizes with confidence intervals at both unit and cell level so that the cost of treating cells as replicates is visible rather than assumed. Sample sizes for a follow-up study are solved from the confidence bound nearer the null instead of the observed point estimate, after Cohen (1988, ISBN:9780805802832). Figures, machine-readable tables and a generated file of every quoted number are emitted from the same objects, and an interactive 'shiny' application provides guided analysis and report export.

Authors:Raban Heller [aut, cre, cph], Leila Schwindling [aut], Alexander Büchner [aut], Lucia Lindenberger [aut], Steffen Müller [aut], Michael Hannemann [aut], Gerhard Achatz [aut], Simone Rothmiller [aut]

cellreportR_0.2.1.9000.tar.gz
cellreportR_0.2.1.9000.zip(r-4.7-any)cellreportR_0.2.1.9000.zip(r-4.6-any)cellreportR_0.2.1.9000.zip(r-4.5-any)
cellreportR_0.2.1.9000.tgz(r-4.6-any)cellreportR_0.2.1.9000.tgz(r-4.5-any)
cellreportR_0.2.1.9000.tar.gz(r-4.7-any)cellreportR_0.2.1.9000.tar.gz(r-4.6-any)
cellreportR_0.2.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cellreportR/json (API)

# Install 'cellreportR' in R:
install.packages('cellreportR', repos = c('https://cttir.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cttir/cellreportr/issues

Pkgdown/docs site:https://cttir.github.io

On CRAN:

Conda:

4.59 score 11 scripts 147 exports 66 dependencies

Last updated from:885a8753f2. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK442
source / vignettesOK280
linux-releaseOK434
macos-releaseOK289
macos-oldrelOK289
windows-develOK382
windows-releaseOK423
windows-oldrelOK365
wasm-releaseOK150

Exports:cr_apply_gatecr_assign_unitscr_auccr_background_subtractcr_balance_cellscr_batch_keycr_batch_referencecr_blocked_effectcr_build_experimentcr_centroid_overlapcr_channelscr_classify_resultcr_column_mapcr_compare_levelscr_compute_metricscr_confusion_matrixcr_conservative_effectcr_correct_batchcr_datasetcr_designcr_dose_responsecr_effect_gridcr_effect_sizecr_enumeratecr_example_designcr_example_experimentcr_example_exportscr_example_filescr_example_pathcr_example_screencr_exclude_smallcr_export_plotscr_export_report_auditcr_export_report_speccr_export_resultscr_export_tablescr_extract_markerscr_figure_captioncr_figure_sizecr_filename_grammarcr_filter_cellscr_finalize_resultcr_fold_changecr_format_intervalcr_format_numbercr_format_percentcr_format_pvaluecr_ic50cr_import_report_speccr_interpretation_lookupcr_lab_reportcr_lab_report_from_evidencecr_linetype_scalecr_linetypescr_logisticcr_macro_namecr_macroscr_macros_fromcr_marker_rulescr_merge_experimentscr_merge_rulescr_n_cellscr_normalizecr_palettecr_parse_pathscr_path_speccr_plot_comparisoncr_plot_dose_responsecr_plot_effect_sizescr_plot_estimatescr_plot_foldchangecr_plot_forestcr_plot_heatmapcr_plot_histogramcr_plot_intensitycr_plot_platecr_plot_qccr_plot_qc_gatecr_plot_qc_summarycr_plot_result_positioncr_plot_roccr_plot_sample_sizecr_plot_scattercr_plot_screencr_plot_spatialcr_plot_specificitycr_plot_stylecr_plot_timelinecr_powercr_power_analysiscr_power_gridcr_print_report_speccr_qc_doubletscr_qc_filtercr_qc_gatecr_qc_gate_impactcr_qc_intensitycr_qc_manualcr_qc_reportcr_qc_summarycr_read_cellprofilercr_read_cellscr_read_designcr_read_exportcr_read_exportscr_read_qupathcr_read_segmantrcr_render_lab_reportcr_render_reportcr_reportcr_report_datacr_report_display_datacr_report_evidencecr_report_hashcr_report_profilecr_report_provenancecr_report_qccr_report_qc_from_logcr_report_review_appcr_report_speccr_report_stylecr_roccr_rowcol_to_wellcr_run_appcr_save_figurecr_save_plotcr_scale_colourcr_scale_divergingcr_scale_fillcr_scale_groupcr_shape_scalecr_shapescr_standardize_batchcr_summarize_wellscr_table_dispositioncr_table_qccr_tablescr_testcr_test_allcr_themecr_unit_mapcr_unit_variabilitycr_validate_experimentcr_validate_report_evidencecr_validate_report_qccr_validate_report_speccr_well_to_rowcol

Dependencies:base64encbitbit64bslibcachemcellrangerclicliprcommonmarkcpp11crayondigestdplyrfarverfastmapfontawesomefsgenericsggplot2gluegtablehmshtmltoolshttpuvisobandjquerylibjsonlitelabelinglaterlifecyclemagrittrmemoisemimeotelpillarpkgconfigprettyunitspROCprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangS7sassscalesshinysourcetoolsstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxtable

Interactive Analysis with the cellreportR Shiny App
Launching | Layout | The sidebar | The tabs | Cross-tab state | Deployment
Rendered fromshiny-app.Rmdusingknitr::rmarkdown

Last update: 2026-10-30
Started: 2026-05-04

Statistical Analysis of Cell-Based Assays
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
Rendered fromstatistical-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-10-30
Started: 2026-05-04

Configurable Laboratory Reports with cellreportR
Report design and document control
Rendered fromlaboratory-reporting.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-08-13

Dose-Response Analysis
Setting up an exposure axis | Fitting | IC50 / EC50 | Plotting | Comparing models | Checking that the fit converged | Where this fits
Rendered fromdose-response.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-05-04

End to End: From Segmented Exports to a Finished Report
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
Rendered fromend-to-end.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-08-13

Getting Started with cellreportR
1. Load example data | 2. Inspect the design | 3. Apply quality control | 4. Fold changes and tests | 5. Visualize | 6. Discriminability | 7. Next steps
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-05-04

Publication-ready figures with cellreportR
Rendered fromfigure-style.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-08-13

Readme and manuals

Help Manual

Help pageTopics
Apply a QC gate to an experimentcr_apply_gate
Assign cells to analysis unitscr_assign_units
Compute AUC with confidence interval from a 'cr_result'cr_auc
Subtract background from a channelcr_background_subtract
Balance the number of cells per analysis unitcr_balance_cells
Construct a batch keycr_batch_key
Per-batch control reference statisticscr_batch_reference
Block-stratified sensitivity fitcr_blocked_effect
Build a 'cr_experiment' objectcr_build_experiment
Centroid overlap between two candidate unitscr_centroid_overlap
List channels in a 'cr_experiment'cr_channels
Deterministically classify numeric results using explicit boundariescr_classify_result
Declare a column contract for vendor exportscr_column_map print.cr_column_map
Compare unit-level and cell-level effect estimatescr_compare_levels
Compute per-unit summary metricscr_compute_metrics
Confusion matrix for a logistic 'cr_result'cr_confusion_matrix
Effect size at the confidence bound nearer the nullcr_conservative_effect
Correct batch effectscr_correct_batch
Build an ingested data setcr_dataset print.cr_dataset summary.cr_dataset
Build an experimental design objectcr_design print.cr_design
Fit a dose-response curvecr_dose_response
Effect sizes for a whole grid of contrastscr_effect_grid
Compute effect sizes between two samplescr_effect_size
Write a vector out as an English listcr_enumerate
Generate an example experimental designcr_example_design
Generate a synthetic 'cr_experiment'cr_example_experiment
Write a synthetic export treecr_example_exports
Write example files in several on-disk formatscr_example_files
Locate the example files shipped with the packagecr_example_path
Generate a synthetic multi-compound screencr_example_screen
Exclude sub-threshold objects with a data-derived cut-offcr_exclude_small
Export plots to PNG, PDF or SVG in batchcr_export_plots
Export report audit provenance as JSONcr_export_report_audit
Export a report specification as versioned JSONcr_export_report_spec
Export results to CSV, Excel or RDScr_export_results
Export a set of tables to CSV or Excelcr_export_tables
Extract file-name markers into typed flagscr_extract_markers
Build a descriptive figure captioncr_figure_caption
Standard deterministic figure dimensionscr_figure_size
Declare the token grammar of an export file namecr_filename_grammar print.cr_filename_grammar
Filter cells in a 'cr_experiment'cr_filter_cells
Apply a caller-selected QC finalization rulecr_finalize_result
Compute fold change relative to a control groupcr_fold_change
Format an estimate and confidence intervalcr_format_interval
Format a number for a generated documentcr_format_number
Format proportions as percentagescr_format_percent
Format p-values without displaying calculated zerocr_format_pvalue
Extract IC50 / EC50 from a dose-response fitcr_ic50
Import a versioned report specification from JSONcr_import_report_spec
Look up explicit interpretation textcr_interpretation_lookup
Assemble a laboratory report without recalculating analytical valuescr_lab_report
Assemble a laboratory report with validated, source-bound quoted valuescr_lab_report_from_evidence
Stable line types for categorical figurescr_linetypes
Univariate logistic regression of treatment vs. controlcr_logistic
Build a macro-safe namecr_macro_name
Emit named values as a generated include filecr_macros
Derive generated numbers from a report or a results tablecr_macros_from
Declare how parenthetical file-name markers are interpretedcr_marker_rules
Merge multiple experimentscr_merge_experiments
Declare how files are merged into analysis unitscr_merge_rules print.cr_merge_rules
Count cells in a 'cr_experiment'cr_n_cells
Normalize intensity datacr_normalize
Colour-vision-safe palettecr_palette
Parse design facts out of export pathscr_parse_paths
Bundle a directory and file-name specificationcr_path_spec print.cr_path_spec
Comparison panel (box, fold change, p-value) for a single resultcr_plot_comparison
Dose-response plotcr_plot_dose_response
Forest plot of effect sizescr_plot_effect_sizes
Plot estimates and confidence intervalscr_plot_estimates
Fold-change forest plotcr_plot_foldchange
Forest plot of effect sizes with confidence intervalscr_plot_forest
Heatmap of channel medians across groupscr_plot_heatmap
Histogram of channel intensitycr_plot_histogram
Intensity distributions by groupcr_plot_intensity
Plate-layout heatmapcr_plot_plate
QC dashboardcr_plot_qc
Quality-control gate diagnostic plotcr_plot_qc_gate
Compact text-first QC status plotcr_plot_qc_summary
Plot a value relative to caller-supplied boundariescr_plot_result_position
ROC curve plotcr_plot_roc
Sample-size comparison plotcr_plot_sample_size
Biaxial scatter plot of two channelscr_plot_scatter
Distribution figure with the unit of replication overlaidcr_plot_screen
Spatial scatter of cells in a wellcr_plot_spatial
Specificity control plotcr_plot_specificity
Construct a reusable plot stylecr_plot_style
Time-course line plotcr_plot_timeline
Sample size for a future study, sized twicecr_power
Simulated power under independent-cell assumptionscr_power_analysis
Sample sizes for a whole effect gridcr_power_grid
Print a laboratory report specificationcr_print_report_spec
Flag or remove doubletscr_qc_doublets
Filter cells by morphologycr_qc_filter
Gate analysis units against their own in-batch controlcr_qc_gate
Quantify the leverage of gate exclusionscr_qc_gate_impact
Gate cells by intensitycr_qc_intensity
Manually exclude wells or cellscr_qc_manual
Report every analysis unit with its QC verdictcr_qc_report
Summarise QC steps applied to an experimentcr_qc_summary
Read a CellProfiler object exportcr_read_cellprofiler
Read segmented cell data from filecr_read_cells
Read experimental design from CSV or Excelcr_read_design
Read one segmented single-cell exportcr_read_export
Read a directory tree of segmented single-cell exportscr_read_exports
Read a QuPath measurement exportcr_read_qupath
Read a segmantR resultcr_read_segmantr
Render a concise laboratory reportcr_render_lab_report
Render a report to HTML or PDFcr_render_report
Assemble a structured analysis reportcr_report
Inspect the exact structured values entering a laboratory reportcr_report_data
Prepare human-facing values for report renderingcr_report_display_data
Bind report claims and figures to portable source-file evidencecr_report_evidence
Hash report-relevant structured datacr_report_hash
Create a reusable laboratory report profilecr_report_profile
Build machine-readable report provenancecr_report_provenance
Construct a concise report QC tablecr_report_qc
Convert an existing experiment QC log to report-compatible rowscr_report_qc_from_log
Review an immutable source-bound report in a Shiny applicationcr_report_review_app
Construct a configurable laboratory report specificationcr_report_spec
Configure the appearance of laboratory reportscr_report_style
Extract or compute an ROC curve from a 'cr_result'cr_roc
Convert row and column indices to well IDscr_rowcol_to_well
Launch the cellreportR Shiny applicationcr_run_app
Save a publication-ready figure deterministicallycr_save_figure
Save a figure at publication settingscr_save_plot
Manual colour scale from the cellreportR visual systemcr_linetype_scale cr_scale_colour cr_scale_fill cr_shape_scale
Continuous diverging scalecr_scale_diverging
Grouping scales with redundant encodingcr_scale_group
Redundant shape encodingcr_shapes
Standardize a channel against the control of each cell's own batchcr_standardize_batch
Summarize cell-level data to the analysis unitcr_summarize_wells
Tabulate how many units and cells entered the analysiscr_table_disposition
Tabulate the quality-control recordcr_table_qc
Collect the tables of an analysiscr_tables
Hypothesis test comparing treatment to controlcr_test
Test all treatments against a control groupcr_test_all
Publication themecr_theme
Map source files to analysis unitscr_unit_map
Between-unit variability within a conditioncr_unit_variability
Validate a 'cr_experiment'cr_validate_experiment
Revalidate report evidence against its current source treecr_validate_report_evidence
Validate a concise report QC tablecr_validate_report_qc
Validate a laboratory report specificationcr_validate_report_spec
Convert well IDs to row and column indicescr_well_to_rowcol
Print method for 'cr_experiment'print.cr_experiment
Print a QC gateprint.cr_qc_gate
Print method for 'cr_report'print.cr_report
Print method for 'cr_result'print.cr_result
Summary method for 'cr_experiment'summary.cr_experiment
Summary method for 'cr_report'summary.cr_report
Summary method for 'cr_result'summary.cr_result