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Lotfollahi-lab / nichecompass

End-to-end analysis of spatial multi-omics data
https://nichecompass.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
36 stars 6 forks source link

Gene program files #75

Closed nimarafati closed 2 months ago

nimarafati commented 2 months ago

Hi,

I would like to use this tool for my project which is human data. I tried to find gene programs but I am not sure whether all the files are in the repo. For example "../data/gene_programs/omnipath_lr_network.csv" . which is loaded in src/nichecompass/utils/gene_programs.py file is not located under the data directory.

In other words, are all the required gene programs: OmniPath (Ligand-Receptor GPs) MEBOCOST (Enzyme-Sensor GPs) NicheNet (Combined Interaction GPs) In the repo under data folder?

sebastianbirk commented 2 months ago

Hello, Thanks for your interest in our tool. If you follow the tutorial here, the gene program files will be downloaded. This is done via the save_to_disk parameter.

nimarafati commented 2 months ago

Thanks Sebastian. I was directly looking into the codes in the cloned repo and missed the link.