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Mass cytometry milestones

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mleipold

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Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Feb 02, 2022 3:52 pm

Mass cytometry milestones

Hi all,

By my count, we have now reached:
1. 1900 mass cytometry papers (including preprints)
2. 505 publicly available mass cytometry datasets (including a few not yet attached to a paper)
3. 262 algorithms used to analyze mass cytometry data (the VAST majority only used once, and counting variations on a theme like the several implementations of tSNE)


Mike
<<

mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Feb 17, 2022 10:14 pm

Re: Mass cytometry milestones

Hi all,

As many of you probably saw, I posted a similar message on my LinkedIn account.

One response I got was "That’s a lot of tools to be used only once. Do you know of any active effort to review and consolidate analysis tools to see which ones are best for common use cases? and/or where gaps remain? We desperately need that."


I thought I'd throw this out to the full reader base:
1. What would you wish to see in such a review and consolidation?
2. Where do you see gaps in data analysis? (note: the answer may differ somewhat between code-savvy people and those of us still dependent on GUIs)

I should say: as much as we'd all like such an answer (myself included), I doubt there's a way to break it down to a flow chart like "if your study looks like <this>, use Algorithm A. If your study looks like <that>, use Algorithm B." Studies are too different (size, number of subgroups, single-timepoint vs timecourse, etc), depend on the research question being asked, or are being coupled with other assays that may impact the way you do your shared analysis.

I'm not sure that cytometry will converge to a small handful of programs like RNAseq has (mostly Seurat.....). But it's been more than 10 years since the 2011-Bendall et al-Science paper (first use of SPADE), and while there are several algorithms that are in wide use (especially FlowSOM and Phenograph), more and more keep coming out......what do you feel is missing?


Mike

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