Add plate 2 feature processing module

WayScience / pyroptosis_signature_image_profiling

This repository contains the pipelines used to analyze the data sets from the Interstellar collaboration.

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Add plate 2 feature processing module #27

Closed jenna-tomkinson closed 1 year ago

jenna-tomkinson commented 1 year ago

In this PR, it includes the notebooks/py files to:

1) Merge and convert single cells from CellProfiler SQLite file to parquet file + add single cell counts per well as metadata column 2) Annotate the merged parquet file with metadata from platemap file 3) Normalize features with negative control 4) Feature select with normalized data

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MikeLippincott commented 1 year ago

LGTM! Minor comments, some doing with future implementations. Cheers! Excited to looks at this data.

jenna-tomkinson commented 1 year ago

@roshankern @MikeLippincott

Thank you both for reviewing this PR. I am going to merge this now after addressing the comments. This will be the last PR for a while in this repo, as we will be working on Alpine implementation to run the PBMCs (TBD).