search

alevax / pyviper

Porting of Protein Activity and Pathway Inference to single cell and Python.
MIT License
4 stars 0 forks source link

network assignment in viper as input #48

Closed LucaZanella15 closed 7 months ago

LucaZanella15 commented 8 months ago

Provide a list of networks to viper as input parameter as an option to run a sort of "network_match_viper". Alternatively, the function can also take the network with the highest enrichment for each cell.

alexanderlewis99 commented 8 months ago

This is a good concept, but should be a feature of another project. This is too complicated for us to put into this particular project as it would take a great deal of work to build this feature and then test it to ensure this feature actually works as we want it to.

alevax commented 8 months ago

We need two features before submitting the paper: 1) a parameter that says which adata.obs column to look for (which should be categorical) in order to perform a manual assignment between cell/sample and network. It basically runs VIPER with a list of networks (and not metaVIPER) by associating each network to each cell/sample based on a label configured in adata.obs and passed as parameter of viper 2) a parameter that says to use enrichment analysis to perform network association. This is more metaVIPER-like, but only the VIPER run per sample that has the highest enrichment across all the network will be retained after the viper run.

alexanderlewis99 commented 7 months ago

Solved by commit 23c56f5