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Karrrramba / HIPrAM

Hydrophobic Interaction Chromatography Protein Profiling with Bayesian Additive Models

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To Do #1

Open Karrrramba opened 6 months ago

Karrrramba commented 6 months ago

Data Prep

[x] Redesign code to read raw maxquant ouptut
[x] Remove duplicate values based on razor/unique peptides
[x] Add missing gene and protein names from UniProt
[x] Collapse protein IDs to gene name
[x] Transform intensities
[x] Profile filtering based on pearson r^2

Performance

[x] Review GAM function
[x] LRT vs. t-test
[ ] Figures
[x] Illustrative example

Analysis

[ ] Add GO annotations
[ ] Protein complex identification
[ ] (Complex co-profiling)
[ ] Network filtering