2024-Liu et al-preprint
"Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating"
Peng Liu, Yuchen Pan, Hung-Ching Chang, Yusi Fang, Xiangning Xue, Jian Zou, Jessica M. Toothaker, Oluwabunmi Olaloye, Eduardo Gonzalez Santiago, Black McCourt, Vanessa Mitsialis, Pietro Presicce, Suhas G. Kallapur, Scott B. Snapper, Jia-Jun Liu, George Tseng, Liza Konnikova, Silvia Liu
bioRxiv, posted August 15, 2024
https://doi.org/10.1101/2024.08.12.607667
- will update when/if this is peer-reviewed and published
- new human PBMC and dataset new Rhesus PBMC dataset accessions not given
- reuses
Rhesus villi: 2020-Toothaker et al-Front Immunol
Human villi: 2022-Toothaker et al-Development
Human bone marrow: 2015-Levine et al-Cell
Mouse bone marrow: 2016-Samusik et al-Nat Methods
GatingMethod, tSNE, ACCENSE, CCAST, ClusterX, Cytometree, densityCUT, DensVM, DEPECHE, FLOCK, flowClust, FlowGrid, flowMeans, flowPeaks, FlowSOM, immunoClust, kmeans, PAC-MAN, Phenograph, Rclusterpp, SamSPECTRAL, SPADE, SWIFT, X-shift, DeepCyTOF, CyTOF linear classifier, ACDC, MP, OpenCyto, flowLearn
Peng Liu, Yuchen Pan, Hung-Ching Chang, Yusi Fang, Xiangning Xue, Jian Zou, Jessica M. Toothaker, Oluwabunmi Olaloye, Eduardo Gonzalez Santiago, Black McCourt, Vanessa Mitsialis, Pietro Presicce, Suhas G. Kallapur, Scott B. Snapper, Jia-Jun Liu, George Tseng, Liza Konnikova, Silvia Liu
bioRxiv, posted August 15, 2024
https://doi.org/10.1101/2024.08.12.607667
- will update when/if this is peer-reviewed and published
- new human PBMC and dataset new Rhesus PBMC dataset accessions not given
- reuses
Rhesus villi: 2020-Toothaker et al-Front Immunol
Human villi: 2022-Toothaker et al-Development
Human bone marrow: 2015-Levine et al-Cell
Mouse bone marrow: 2016-Samusik et al-Nat Methods
GatingMethod, tSNE, ACCENSE, CCAST, ClusterX, Cytometree, densityCUT, DensVM, DEPECHE, FLOCK, flowClust, FlowGrid, flowMeans, flowPeaks, FlowSOM, immunoClust, kmeans, PAC-MAN, Phenograph, Rclusterpp, SamSPECTRAL, SPADE, SWIFT, X-shift, DeepCyTOF, CyTOF linear classifier, ACDC, MP, OpenCyto, flowLearn