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mckellardw / scMuscle

The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data
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Helper functions for DoubletFinder #1

Closed ccruizm closed 3 years ago

ccruizm commented 3 years ago

Hello @mckellardw!

Thanks for making your code available. Great work! I was looking at how to automate the DoubletFinder pipeline and I saw your nice script. However, I could not find the helper functions for this part of the pipeline in your helper_functions_v1.R file. Could you share them, please?

Thanks in advance!

mckellardw commented 3 years ago

Sorry about that! helper_functions_v1.R is updated to include those two functions. They include a function to estimate the doublet rate in a count matrix (specifically from 10x chromium data), and two of the DoubletFinder functions with a little bit extra functionality (mostly just the ability to specify the column name in the Seurat object where doublet status and pANN output are stored. This makes merging/integrating many datasets much cleaner as each of them will have slightly different parameterization, which by default will show up in those metadata col names).

ccruizm commented 3 years ago

Thank you very much for updating the file! Will give it a try.