cellreportR 0.1.0
Initial release
cellreportR provides an end-to-end analysis and reporting pipeline for cell-culture microscopy assays, picking up where cell segmentation (e.g. segmantR, CellProfiler, QuPath) leaves off.
Core features
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Import:
cr_read_cells(),cr_read_design(),cr_read_cellprofiler(),cr_read_qupath(),cr_read_segmantr(),cr_build_experiment(),cr_validate_experiment(). -
Quality control:
cr_qc_filter(),cr_qc_doublets(),cr_qc_intensity(),cr_qc_manual(),cr_qc_summary(). -
Normalization:
cr_normalize(),cr_background_subtract(),cr_correct_batch(). -
Quantification:
cr_summarize_wells(),cr_fold_change(),cr_compute_metrics(). -
Statistical testing:
cr_test(),cr_test_all(),cr_effect_size(),cr_power_analysis()— hierarchical tests at cell or replicate level with effect sizes. -
Discriminability:
cr_logistic(),cr_roc(),cr_auc(),cr_confusion_matrix(). -
Dose-response:
cr_dose_response()(4PL / 3PL / linear),cr_ic50(). -
Visualization: thirteen
cr_plot_*functions covering plate layouts, distributions, scatter plots, fold-change and effect-size forest plots, ROC curves, dose-response, QC dashboards, spatial plots, heatmaps and time courses. -
Reporting:
cr_report(),cr_export_results(),cr_export_plots(). -
Interactive:
cr_run_app()launches a seven-tab Shiny application. -
Example data:
cr_example_experiment(),cr_example_design(),cr_example_files(). -
Utilities:
cr_well_to_rowcol(),cr_rowcol_to_well(),cr_channels(),cr_n_cells(),cr_filter_cells(),cr_merge_experiments().