MuPETFlow: multiple ploidy estimation tool from flow cytometry data.

Abstract

Background Ploidy, representing the number of homologous chromosome sets, can be estimated from flow cytometry data acquired on cells stained with a fluorescent DNA dye. This estimation relies on a combination of tools that often require scripting, individual sample curation, and additional analyses. Results To automate the ploidy estimation for multiple flow cytometry files, we developed MuPETFlow-a Shiny graphical user interface tool. MuPETFlow allows users to visualize cell fluorescence histograms, detect the peaks corresponding to the different cell cycle phases, perform a linear regression using standards, make ploidy or genome size predictions, and export results as figures and table files. The tool was benchmarked with known ploidy datasets from yeast and plant species, yielding consistent ploidy results. MuPETFlow's peaks detection and performance were also compared to those of other tools. Conclusions MuPETFlow stands out as the only tool offering in-app ploidy detection, multiple peak detection, multi-sample visualization, and automation capabilities. These features significantly accelerate the analysis, making it especially valuable for projects involving large datasets.

Plant phenotyping relevance

植物のフローサイトメトリーデータから倍数性・ゲノムサイズを推定する解析ツールを開発し、植物データセットでベンチマークしているため、植物表現型取得・解析手法が中心である。

Code and data availability

The paper's flow cytometry analysis assets are publicly available: the authors' MuPETFlow GitHub repository hosts the tool code and the newly generated S. cerevisiae FCS datasets, and the plant (Solanum pseudocapsicum) flow cytometry data used for ploidy estimation is deposited in FlowRepository under FR-FCM-Z45W. The