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FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows.

Publication ,  Journal Article
White, S; Quinn, J; Enzor, J; Staats, J; Mosier, SM; Almarode, J; Denny, TN; Weinhold, KJ; Ferrari, G; Chan, C
Published in: Front Immunol
2021

An important challenge for primary or secondary analysis of cytometry data is how to facilitate productive collaboration between domain and quantitative experts. Domain experts in cytometry laboratories and core facilities increasingly recognize the need for automated workflows in the face of increasing data complexity, but by and large, still conduct all analysis using traditional applications, predominantly FlowJo. To a large extent, this cuts domain experts off from the rapidly growing library of Single Cell Data Science algorithms available, curtailing the potential contributions of these experts to the validation and interpretation of results. To address this challenge, we developed FlowKit, a Gating-ML 2.0-compliant Python package that can read and write FCS files and FlowJo workspaces. We present examples of the use of FlowKit for constructing reporting and analysis workflows, including round-tripping results to and from FlowJo for joint analysis by both domain and quantitative experts.

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Published In

Front Immunol

DOI

EISSN

1664-3224

Publication Date

2021

Volume

12

Start / End Page

768541

Location

Switzerland

Related Subject Headings

  • Workflow
  • Software
  • Single-Cell Analysis
  • Machine Learning
  • Humans
  • Flow Cytometry
  • Computational Biology
  • Algorithms
  • 3204 Immunology
  • 3105 Genetics
 

Citation

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White, S., Quinn, J., Enzor, J., Staats, J., Mosier, S. M., Almarode, J., … Chan, C. (2021). FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows. Front Immunol, 12, 768541. https://doi.org/10.3389/fimmu.2021.768541
White, Scott, John Quinn, Jennifer Enzor, Janet Staats, Sarah M. Mosier, James Almarode, Thomas N. Denny, Kent J. Weinhold, Guido Ferrari, and Cliburn Chan. “FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows.Front Immunol 12 (2021): 768541. https://doi.org/10.3389/fimmu.2021.768541.
White S, Quinn J, Enzor J, Staats J, Mosier SM, Almarode J, et al. FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows. Front Immunol. 2021;12:768541.
White, Scott, et al. “FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows.Front Immunol, vol. 12, 2021, p. 768541. Pubmed, doi:10.3389/fimmu.2021.768541.
White S, Quinn J, Enzor J, Staats J, Mosier SM, Almarode J, Denny TN, Weinhold KJ, Ferrari G, Chan C. FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows. Front Immunol. 2021;12:768541.

Published In

Front Immunol

DOI

EISSN

1664-3224

Publication Date

2021

Volume

12

Start / End Page

768541

Location

Switzerland

Related Subject Headings

  • Workflow
  • Software
  • Single-Cell Analysis
  • Machine Learning
  • Humans
  • Flow Cytometry
  • Computational Biology
  • Algorithms
  • 3204 Immunology
  • 3105 Genetics