cellreportR: Cell Culture Microscopy Assay Analysis and Reporting

The cellreportR package provides a complete pipeline for analyzing cell culture-based laboratory assays evaluated by microscopy. It picks up where cell segmentation tools (e.g. segmantR, CellProfiler, QuPath) leave off, and covers experimental design, quality control, normalization, hierarchical statistical testing, effect size estimation, discriminability analysis, and structured report generation.

A companion interactive shiny application is available via cr_run_app() for guided analysis by laboratory personnel.

Typical workflow

1. Read segmented cell data with cr_read_cells() or cr_read_cellprofiler() / cr_read_qupath() / cr_read_segmantr().

2. Assemble with design and channel metadata via cr_build_experiment().

3. Apply quality control (cr_qc_filter(), cr_qc_doublets(), cr_qc_intensity()).

4. Normalize (cr_normalize(), cr_background_subtract()).

5. Quantify (cr_summarize_wells(), cr_fold_change(), cr_compute_metrics()).

6. Test (cr_test(), cr_test_all(), cr_effect_size()).

7. Visualize with any cr_plot_* function.

8. Report via cr_report().

See also

Useful links:

• https://github.com/CTTIR/cellreportR

• https://cttir.github.io/cellreportR/

• Report bugs at https://github.com/CTTIR/cellreportR/issues

Author

Maintainer: Raban Heller raban.heller@charite.de (ORCID) [copyright holder]

Authors:

• Raban Heller raban.heller@charite.de (ORCID) [copyright holder]

• Leila Schwindling

• Alexander Büchner

• Lucia Lindenberger

• Steffen Müller

• Michael Hannemann

• Gerhard Achatz

• Simone Rothmiller