Package index • cellreportR

Import & Build

cr_read_cells(): Read segmented cell data from file
cr_read_design(): Read experimental design from CSV or Excel
cr_read_cellprofiler(): Read CellProfiler output
cr_read_qupath(): Read QuPath measurement export
cr_read_segmantr(): Read segmantR output
cr_build_experiment(): Build a cr_experiment object
cr_validate_experiment(): Validate a cr_experiment

Quality Control

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

Normalization

cr_normalize(): Normalize intensity data
cr_background_subtract(): Subtract background from a channel
cr_correct_batch(): Correct batch effects

Quantification

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

Statistical Analysis

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_power_analysis(): Post-hoc power for a hierarchical cell-based assay

Discriminability

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

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

Visualization

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_roc(): ROC curve plot
cr_plot_dose_response(): Dose-response plot
cr_plot_qc(): QC dashboard
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

Reporting

cr_report(): Generate a structured analysis report
cr_export_results(): Export results to CSV, Excel or RDS
cr_export_plots(): Export plots to PNG, PDF or SVG in batch

Shiny App

cr_run_app(): Launch the cellreportR Shiny application

Example Data

cr_example_experiment(): Generate a synthetic cr_experiment
cr_example_design(): Generate an example experimental design
cr_example_files(): Write example files in multiple formats to a directory

Utilities

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

S3 methods

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