oidyPeaks: R package for automated flow cytometry cell cycle analysis and visualization in fungal microbes

ploidyPeaks enables automated identification and quantification of karyotypic subpopulations from flow cytometry by detecting G0/G1 and G2/M peaks and fitting the Dean-Jett-Fox model with confidence.

• Why it matters: Mixed-karyotype fungal populations are hard to analyze because existing genome-size models assume a single base ploidy, forcing manual gating that can bias subpopulation abundance estimates.
• What they did: The open-source R package ploidyPeaks imports standard .fcs files, uses reference ploidy populations to set thresholds for mixed samples, then applies peak detection and nonlinear least-squares Dean-Jett-Fox fitting to each subpopulation.
• The result: Applied to 240 replicate populations from 20 Candida albicans genetic backgrounds evolving for 100 generations under fluconazole, it quantifies genome size in mixed-karyotype samples without manual intervention and provides an objective model-fit measure.

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