Package index • cellreportR

Ingest

Read segmented single-cell exports and recover the experimental design from the directory tree and the file naming convention.

cr_read_cells(): Read segmented cell data from file
cr_read_design(): Read experimental design from CSV or Excel
cr_read_export(): Read one segmented single-cell export
cr_read_exports(): Read a directory tree of segmented single-cell exports
cr_read_cellprofiler(): Read a CellProfiler object export
cr_read_qupath(): Read a QuPath measurement export
cr_read_segmantr(): Read a segmantR result
cr_column_map() print(<cr_column_map>): Declare a column contract for vendor exports
cr_path_spec() print(<cr_path_spec>): Bundle a directory and file-name specification
cr_parse_paths(): Parse design facts out of export paths
cr_filename_grammar() print(<cr_filename_grammar>): Declare the token grammar of an export file name
cr_marker_rules(): Declare how parenthetical file-name markers are interpreted
cr_extract_markers(): Extract file-name markers into typed flags

Experiment object

Build, validate and inspect the container that carries cells, design, channels, batch keys and provenance.

cr_build_experiment(): Build a cr_experiment object
cr_validate_experiment(): Validate a cr_experiment
cr_dataset() print(<cr_dataset>) summary(<cr_dataset>): Build an ingested data set
cr_design() print(<cr_design>): Build an experimental design object
cr_batch_key(): Construct a batch key
cr_channels(): List channels in a cr_experiment
cr_n_cells(): Count cells in a cr_experiment
cr_filter_cells(): Filter cells in a cr_experiment
cr_merge_experiments(): Merge multiple experiments

Units and balancing

Resolve acquisitions into the analysis unit of replication, then equalise the cell contribution of each unit.

cr_merge_rules() print(<cr_merge_rules>): Declare how files are merged into analysis units
cr_assign_units(): Assign cells to analysis units
cr_unit_map(): Map source files to analysis units
cr_centroid_overlap(): Centroid overlap between two candidate units
cr_exclude_small(): Exclude sub-threshold objects with a data-derived cut-off
cr_balance_cells(): Balance the number of cells per analysis unit

Quality control

Threshold filters, the biological gate against each unit’s own control, and the leverage of what the gate removed.

cr_qc_filter(): Filter cells by morphology
cr_qc_doublets(): Flag or remove doublets
cr_qc_intensity(): Gate cells by intensity
cr_qc_manual(): Manually exclude wells or cells
cr_qc_summary(): Summarise QC steps applied to an experiment
cr_qc_gate(): Gate analysis units against their own in-batch control
cr_qc_gate_impact(): Quantify the leverage of gate exclusions
cr_apply_gate(): Apply a QC gate to an experiment
cr_qc_report(): Report every analysis unit with its QC verdict

Normalization and batch standardization

Rescale each cell against the control condition of its own batch.

cr_normalize(): Normalize intensity data
cr_background_subtract(): Subtract background from a channel
cr_correct_batch(): Correct batch effects
cr_batch_reference(): Per-batch control reference statistics
cr_standardize_batch(): Standardize a channel against the control of each cell's own batch

Quantification

Collapse cells to units and derive per-unit quantities.

cr_summarize_wells(): Summarize cell-level data to the analysis unit
cr_fold_change(): Compute fold change relative to a control group
cr_compute_metrics(): Compute per-unit summary metrics

Effect sizes and testing

Estimate effects with confidence intervals at unit and at cell level, and quantify the distance between the two.

cr_test(): Hypothesis test comparing treatment to control
cr_test_all(): Test all treatments against a control group
cr_effect_size(): Compute effect sizes between two samples
cr_effect_grid(): Effect sizes for a whole grid of contrasts
cr_compare_levels(): Compare unit-level and cell-level effect estimates
cr_blocked_effect(): Block-stratified sensitivity fit
cr_unit_variability(): Between-unit variability within a condition

Sample size

Solve the design for the observed estimate and for the confidence bound nearer the null.

cr_conservative_effect(): Effect size at the confidence bound nearer the null
cr_power(): Sample size for a future study, sized twice
cr_power_grid(): Sample sizes for a whole effect grid
cr_power_analysis(): Post-hoc power for a hierarchical cell-based assay

Discriminability

Logistic models, ROC curves and classification summaries.

cr_logistic(): Univariate logistic regression of treatment vs. control
cr_roc(): Extract or compute an ROC curve from a cr_result
cr_auc(): Compute AUC with confidence interval from a cr_result
cr_confusion_matrix(): Confusion matrix for a logistic cr_result

Dose-response

Concentration-response curve fitting and potency estimates.

cr_dose_response(): Fit a dose-response curve
cr_ic50(): Extract IC50 / EC50 from a dose-response fit

Visualization

Publication figures and the shared plot design contract.

cr_plot_plate(): Plate-layout heatmap
cr_plot_intensity(): Intensity distributions by group
cr_plot_scatter(): Biaxial scatter plot of two channels
cr_plot_histogram(): Histogram of channel intensity
cr_plot_foldchange(): Fold-change forest plot
cr_plot_effect_sizes(): Forest plot of effect sizes
cr_plot_forest(): Forest plot of effect sizes with confidence intervals
cr_plot_screen(): Distribution figure with the unit of replication overlaid
cr_plot_sample_size(): Sample-size comparison plot
cr_plot_specificity(): Specificity control plot
cr_plot_qc(): QC dashboard
cr_plot_qc_gate(): Quality-control gate diagnostic plot
cr_plot_roc(): ROC curve plot
cr_plot_dose_response(): Dose-response plot
cr_plot_spatial(): Spatial scatter of cells in a well
cr_plot_comparison(): Comparison panel (box, fold change, p-value) for a single result
cr_plot_heatmap(): Heatmap of channel medians across groups
cr_plot_timeline(): Time-course line plot
cr_theme(): Publication theme
cr_palette(): Colour-vision-safe palette
cr_shapes(): Redundant shape encoding
cr_scale_group(): Grouping scales with redundant encoding
cr_save_plot(): Save a figure at publication settings

Tables and reporting

Emit every reported count and table from the analysis objects rather than by hand.

cr_tables(): Collect the tables of an analysis
cr_table_disposition(): Tabulate how many units and cells entered the analysis
cr_table_qc(): Tabulate the quality-control record
cr_export_tables(): Export a set of tables to CSV or Excel
cr_export_results(): Export results to CSV, Excel or RDS
cr_export_plots(): Export plots to PNG, PDF or SVG in batch
cr_report(): Assemble a structured analysis report
cr_render_report(): Render a report to HTML or PDF

Generated numbers

Write every quoted number and computed enumeration into a single generated include file.

cr_macros(): Emit named values as a generated include file
cr_macros_from(): Derive generated numbers from a report or a results table
cr_macro_name(): Build a macro-safe name
cr_format_number(): Format a number for a generated document
cr_enumerate(): Write a vector out as an English list

Example data

Synthetic inputs that exercise the whole pipeline.

cr_example_screen(): Generate a synthetic multi-compound screen
cr_example_experiment(): Generate a synthetic cr_experiment
cr_example_design(): Generate an example experimental design
cr_example_exports(): Write a synthetic export tree
cr_example_files(): Write example files in several on-disk formats
cr_example_path(): Locate the example files shipped with the package

Plate utilities

Coordinate helpers for plate layouts.

cr_well_to_rowcol(): Convert well IDs to row and column indices
cr_rowcol_to_well(): Convert row and column indices to well IDs

Interactive front-end

Guided analysis, exploration and report export in the browser.

cr_run_app(): Launch the cellreportR Shiny application

Methods

Print and summarise the objects the pipeline returns.

print(<cr_experiment>): Print method for cr_experiment
summary(<cr_experiment>): Summary method for cr_experiment
print(<cr_result>): Print method for cr_result
summary(<cr_result>): Summary method for cr_result
print(<cr_report>): Print method for cr_report
summary(<cr_report>): Summary method for cr_report
print(<cr_qc_gate>): Print a QC gate

Package

cellreportR-package cellreportR: cellreportR: Cell Culture Microscopy Assay Analysis and Reporting