HiTMapper Comparisons

Comparison of HiTMapper with manual gating and other algorithms as well as several analysis perspectives

Dataset	Cytometry Modality	Description	Reference
Levine Benchmark Data	Mass Cytometry (CyTOF)	The data set is a 32-dimensional mass cytometry (CyTOF) data set, consisting of protein expression levels for n = 265,627 cells, p = 32 protein markers (dimensions), and k = 14 manually gated cell populations (clusters), from h = 2 individuals. Cluster labels are available for 39% (104,184) of the cells.	Levine et al. (2015)
Acute COVID (Day ?)	Mass Cytometry (CyTOF)	Small subset of the acute COVID flow cytometry data	Mathew, Giles, Baxter, Oldridge, Greenplate, Wu, Alanio, et al. (2020)
COVID Vaccine (Day ?)	Mass Cytometry (CyTOF)	Description	Mathew, Giles, Baxter, Oldridge, Greenplate, Wu, Alanio, et al. (2020)
Acute COVID (Day 0 and Day 7)	Mass Cytometry (CyTOF)	Description	Mathew, Giles, Baxter, Oldridge, Greenplate, Wu, Alanio, et al. (2020)

Comparison of HiTMapper, FlowSOM, Rphenograph, and FastPG using 32-dimensional CyTOF data from Levine et al

Method	Description	Reference	GitHub
HiTMapper	Description	Version	HiTMapper Code
FlowSOM	Description	Version	FlowSOM Code
Rphenograph	Description	Version	Rphenograph Code
FastPG	Description	Version	FastPG Code

• Additionally, there's a command-line implementation of FastPG by MCMICRO, https://github.com/labsyspharm/mcmicro-fastPG

Mass Cytometry (CyTOF) data analysis using HiTMapper

• Led by Matei Ionita
• Acute COVID (Day ?)
• COVID Vaccine (Day ?)

Flow Cytometry data analysis using HiTMapper

• Led by Van Truong
• Acute Covide (Day 0 and Day 7)