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morris-lab / BiddyetalWorkflow

This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
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iEP QuadProg code #7

Closed sachitsaksena closed 3 months ago

sachitsaksena commented 3 months ago

Hi all, thanks for the great paper on CellTag. In what script is the iEP identity score computed as described in Biddy et al. 2018: "The R package QuadProg was used for quadratic programming to generate cell identity scores."?

Thanks for the help!

sam-morris commented 3 months ago

Hi - I just uploaded a R markdown file to https://github.com/morris-lab/BiddyetalWorkflow/tree/master/scripts. You might also want to take a look at https://github.com/morris-lab/Capybara, which is based on the QP approach.

sachitsaksena commented 3 months ago

Thank you @sam-morris! And will do.

sachitsaksena commented 3 months ago

Sorry, just took a look and the imported script: "/scratch/smlab/CellTag_paper_analysis/quad_prog/src/quad_prog_collective_functions.R" is not available.

Alternatively, if you could point me to the metadata with iEP identity scores generated for Figure 1f of the 10X timecourse in the paper, that would be helpful!

Thanks again @sam-morris!