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flowDiv: a new pipeline for analyzing flow cytometric diversity.

Bruno M S Wanderley1,2, Daniel S A Araújo1, María V Quiroga3

  • 1Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal, Brazil.

BMC Bioinformatics
|May 30, 2019
PubMed
Summary

A new R pipeline, flowDiv, addresses challenges in analyzing environmental flow cytometry (FCM) data. It integrates diverse datasets and explores cytometric diversity in freshwater lakes, offering a unified approach for environmental science.

Keywords:
Cytometric diversityFlow cytometryR language

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Area of Science:

  • Environmental Science
  • Ecology
  • Limnology

Background:

  • Flow cytometry (FCM) is a versatile tool for cellular analysis, but protocols are often not interchangeable across disciplines.
  • Environmental science struggles with FCM due to sample heterogeneity, complicating data analysis and interpretation of cytometric diversity.
  • Existing bioinformatic tools for cytometric diversity face challenges with data integration and population correlation.

Purpose of the Study:

  • To develop an R language pipeline, flowDiv, for analyzing environmental flow cytometry data.
  • To address technical issues in FCM data analysis, including dataset integration and binning strategies.
  • To provide a framework for exploring cytometric diversity in environmental samples.

Main Methods:

  • Development of flowDiv, an R pipeline specifically for environmental FCM data.
  • Application of flowDiv to a dataset from 31 freshwater lakes in Patagonia, Argentina.
  • Utilizing cytometric diversity analysis to interpret biological patterns.

Main Results:

  • flowDiv successfully integrates and analyzes environmental FCM data.
  • Significant aspects of cytometric diversity were revealed in the Patagonian freshwater lake dataset.
  • The pipeline facilitates the evaluation of differences between cytograms.

Conclusions:

  • flowDiv offers an intuitive framework for FCM analysis, merging mathematical rigor with biological relevance.
  • The pipeline is specifically designed to enhance the exploration of cytometric diversity in environmental contexts.
  • flowDiv provides a practical solution for common challenges in analyzing heterogeneous environmental FCM data.