chenyenchung / scmarco

Interactive visualization of binarized gene expression for combinatorial marker discovery

Hi there 👋

I am a PhD candidate in the Desplan lab at New York University. I study genetic programs that specify different kind of neurons in development. Using fly visual system as my model, I’m currently studying how early patterning events are translated into the making of different cells using single-cell transcriptomics. While still trying to get a hold of it, I am generally interested in statistics and interpretable machine learning.

Besides the links in my profile, you can also find me on Mastodon.

scmarco's Issues

Generating mixture model data

Thanks for making this tool! I am interested in using this on my own single cell dataset. However, I haven't been able to calculate gene expression probability for identified clusters.

The documentation begins assuming that you have previously calculated modeled expression probability. In the paper, it looks like the code from Davis et al., 2020 was used to get these modeled probabilities. Is that correct?

I have had trouble using that code on my own data, since I don't know how to format my data. Can you provide an example on how to use the code in analyzeOpticLobeExpr.R?

Thank you,

Peter