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...
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BMC
2025-03-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11470-8 |
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| author | C. Gómez-Muñoz G. Fischer |
| author_facet | C. Gómez-Muñoz G. Fischer |
| author_sort | C. Gómez-Muñoz |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-dda74a01179f434281e0beafd459d82d |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-dda74a01179f434281e0beafd459d82d2025-08-20T03:40:46ZengBMCBMC Genomics1471-21642025-03-012611510.1186/s12864-025-11470-8MuPETFlow: multiple ploidy estimation tool from flow cytometry dataC. Gómez-Muñoz0G. Fischer1Laboratory of Computational, Quantitative and Synthetic Biology (CQSB), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Sorbonne UniversitéLaboratory of Computational, Quantitative and Synthetic Biology (CQSB), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Sorbonne UniversitéAbstract 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.https://doi.org/10.1186/s12864-025-11470-8CytometryPloidyGenomeSoftwareGraphical user interface |
| spellingShingle | C. Gómez-Muñoz G. Fischer MuPETFlow: multiple ploidy estimation tool from flow cytometry data BMC Genomics Cytometry Ploidy Genome Software Graphical user interface |
| title | MuPETFlow: multiple ploidy estimation tool from flow cytometry data |
| title_full | MuPETFlow: multiple ploidy estimation tool from flow cytometry data |
| title_fullStr | MuPETFlow: multiple ploidy estimation tool from flow cytometry data |
| title_full_unstemmed | MuPETFlow: multiple ploidy estimation tool from flow cytometry data |
| title_short | MuPETFlow: multiple ploidy estimation tool from flow cytometry data |
| title_sort | mupetflow multiple ploidy estimation tool from flow cytometry data |
| topic | Cytometry Ploidy Genome Software Graphical user interface |
| url | https://doi.org/10.1186/s12864-025-11470-8 |
| work_keys_str_mv | AT cgomezmunoz mupetflowmultipleploidyestimationtoolfromflowcytometrydata AT gfischer mupetflowmultipleploidyestimationtoolfromflowcytometrydata |