FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows
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 increa...
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Frontiers Media S.A.
2021
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oai:doaj.org-article:11790a03c6cc4f8c9b82133b4ac970722021-11-05T14:45:31ZFlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows1664-322410.3389/fimmu.2021.768541https://doaj.org/article/11790a03c6cc4f8c9b82133b4ac970722021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fimmu.2021.768541/fullhttps://doaj.org/toc/1664-3224An 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.Scott WhiteScott WhiteScott WhiteJohn QuinnJennifer EnzorJennifer EnzorJanet StaatsJanet StaatsSarah M. MosierSarah M. MosierJames AlmarodeThomas N. DennyThomas N. DennyKent J. WeinholdKent J. WeinholdKent J. WeinholdGuido FerrariGuido FerrariGuido FerrariCliburn ChanCliburn ChanCliburn ChanFrontiers Media S.A.articlesystems immunologyflow cytometrysoftwarepython (programming language)single cell data scienceFlowJoImmunologic diseases. AllergyRC581-607ENFrontiers in Immunology, Vol 12 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
systems immunology flow cytometry software python (programming language) single cell data science FlowJo Immunologic diseases. Allergy RC581-607 |
| spellingShingle |
systems immunology flow cytometry software python (programming language) single cell data science FlowJo Immunologic diseases. Allergy RC581-607 Scott White Scott White Scott White John Quinn Jennifer Enzor Jennifer Enzor Janet Staats Janet Staats Sarah M. Mosier Sarah M. Mosier James Almarode Thomas N. Denny Thomas N. Denny Kent J. Weinhold Kent J. Weinhold Kent J. Weinhold Guido Ferrari Guido Ferrari Guido Ferrari Cliburn Chan Cliburn Chan Cliburn Chan FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows |
| description |
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. |
| format |
article |
| author |
Scott White Scott White Scott White John Quinn Jennifer Enzor Jennifer Enzor Janet Staats Janet Staats Sarah M. Mosier Sarah M. Mosier James Almarode Thomas N. Denny Thomas N. Denny Kent J. Weinhold Kent J. Weinhold Kent J. Weinhold Guido Ferrari Guido Ferrari Guido Ferrari Cliburn Chan Cliburn Chan Cliburn Chan |
| author_facet |
Scott White Scott White Scott White John Quinn Jennifer Enzor Jennifer Enzor Janet Staats Janet Staats Sarah M. Mosier Sarah M. Mosier James Almarode Thomas N. Denny Thomas N. Denny Kent J. Weinhold Kent J. Weinhold Kent J. Weinhold Guido Ferrari Guido Ferrari Guido Ferrari Cliburn Chan Cliburn Chan Cliburn Chan |
| author_sort |
Scott White |
| title |
FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows |
| title_short |
FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows |
| title_full |
FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows |
| title_fullStr |
FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows |
| title_full_unstemmed |
FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows |
| title_sort |
flowkit: a python toolkit for integrated manual and automated cytometry analysis workflows |
| publisher |
Frontiers Media S.A. |
| publishDate |
2021 |
| url |
https://doaj.org/article/11790a03c6cc4f8c9b82133b4ac97072 |
| work_keys_str_mv |
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