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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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Sample method blurb for CATALYST? #399

Closed denvercal1234GitHub closed 4 months ago

denvercal1234GitHub commented 4 months ago

Hi there,

Thank you for a great package!

The tutorial at https://bioconductor.org/packages/release/workflows/vignettes/cytofWorkflow/inst/doc/cytofWorkflow.html#data-preprocessing is very useful already, but I wonder if there might exist a sample blurb for the clustering and differential expressed protein analysis workflow for CATALYST?

Thank you again!

HelenaLC commented 4 months ago

Hey! Thanks for the compliment. Can you be a little more specific, i.e., what do you mean exactly by „blurb“? By now, there are 2 vignettes & 3 publications associated with the methodology in CATALYST; the clustering has been published previously by an independent group

denvercal1234GitHub commented 4 months ago

Thank you for your response, Helena.

I am writing my method section for my paper that uses CATALYST to cluster flow data, and I was just wondering if there is a sample description of workflow adapted for flow data that I could compare with how others who have used the package for flow data describe the different steps.

Most publications using CATALYST understandably describes mass spec workflow, e.g., https://doi.org/10.1016/j.isci.2024.109882 or https://doi.org/10.1016/j.isci.2024.109032, and tbh they are quite too brief.

I will adapt these mass spec ones for my method writeup, but just wondering.

HelenaLC commented 4 months ago

To avoid confusion: CATALYST was designed for mass cytometry (not spectrometry) data.

I see. To my understanding (and having been involved in a pub that used FACS), the only difference lies in quality control (e.g., using forward/side scatter that are absent in CyTOF) & normalization (e.g., different cofactor). Clustering and differential testing should be applicable in the same way. Then again, if your already writing, you should describe your methods.

GitHub issues are meant for software- and methodology-related issues/questions/suggestions, which developers try to resolve “on their own time”, while maintaining software over many years… I hope for your understanding.

denvercal1234GitHub commented 4 months ago

Thank you Helena. This is very useful!