In collaboration with the Van Ry and Kelly labs at BYU.
If you're new to this project, there's a Google Doc and Google Drive folder with detail information about where we are and what to do next. Talk with Sam if you don't have it.
A lot analysis functions for this project are contained within a Python package included in the repository called oscutils (Organoid Single-Cell UTILitieS). To install and use it, follow the instructions in oscutils/README.md.
If you delve into the depths of this repo, you will notice that the data were ran twice each with both Proteome Discoverer and MetaMorpheus. However, the older run from each software has issues--specifically, the older PD run is missing one of the pseudo-bulk samples, and the older MM run included the blank, contaminated, no protein, and QC samples, which we found out later can mess up the normalization that MM does, so we ran it again without those samples.
So, even though those older data exist, you shouldn't use them for analysis. The oscutils package is set up to load the newer runs by default, and you should only use those.