KIC Spheroid Calcium Pipeline (Script 03/03) – Statistical Analysis & Visualization

KIC Spheroid Calcium Pipeline — Script 03/03 GUI-based R pipeline for performing peak-quality filtering, statistical testing, and generating publication-ready bar plots from merged calcium datasets generated in Script 02a or Script 02b. What's included GUI selection of input file and output folder Optional selection of specific Batch and Group values User-defined group ordering Strict peak-quality filtering based on expected frequency and tolerance (%) Automatic numeric coercion and column harmonization Within-group outlier detection (1.5×IQR rule) Generation of standardized bar plots (Mean ± SD + individual wells) Statistical testing (Welch t-test or one-way ANOVA + Tukey post-hoc) Automatic significance annotation (*, **, ***, ****) Export of plots in high-resolution PNG and vector PDF formats Diagnostic and filtering reports Inputs merged.csv (generated in Script 02a) or merged_raw.csv (generated in Script 02b) Required columns: Well Group Num.Peaks If multi-batch: Batch Optional but recommended: RowGroup keep_1hz valid_well Outputs *.png — High-resolution statistical plots *.pdf — Vector publication-ready plots plot_diagnostics.csv — Per-metric plotting summary outliers_removed.csv — IQR-filtered values peak_filter_log.csv — Peak filtering report Outputs are standardized for reproducible statistical comparison and cross-experiment consistency. Citation Developed by Michele Buono, Talitha Spanjersberg, Nikki Scheen, and Nina van der Wilt. Free for research use and adaptation with citation via Zenodo.