cellreportR is a complete analysis and reporting pipeline for routine cell-culture laboratory diagnostics with microscopic evaluation. It picks up where segmentation leaves off: segmented single-cell data flows in, and structured statistical analyses, quality-controlled results, and publication- and audit-ready reports flow out.
Cell culture -> Treatment -> Staining -> Microscopy -> Segmentation
(segmantR / CellProfiler / QuPath)
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v
+---------------------+
| cellreportR |
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| Design & QC |
| Normalization |
| Hierarchical tests |
| Effect sizes + ROC |
| Dose-response |
| Visualization |
| Report generation |
| Shiny dashboard |
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v
Structured diagnostic report
# install.packages("pak")
pak::pak("r-heller/cellreportR")library(cellreportR)
exp <- cr_example_experiment(seed = 42)
exp <- cr_qc_filter(exp, min_area = 50, max_area = 5000)
res <- cr_test_all(exp,
channel = "marker_1",
control_group = "Untreated",
level = "replicate")
cr_plot_effect_sizes(res)cr_run_app()The Shiny app provides a guided seven-tab workflow covering data import, QC, normalization, statistical analysis, dose-response fitting, interactive visualisation and report generation.
If you use cellreportR in your research, please cite the package:
citation("cellreportR")