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dpeerlab / Palantir

Single cell trajectory detection
https://palantir.readthedocs.io
GNU General Public License v2.0
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PackageNotInstalledError: The R package "gam" is not installed. #45

Closed zmokhtari closed 4 years ago

zmokhtari commented 4 years ago

Hi, Even though I have installed "gam" in R, I still face this issue: "PackageNotInstalledError: The R package "gam" is not installed " when I try to determine the gene expression trends. Would it be possible to use "pygam" instead of "gam" from R?

Thanks, Zeinab

ManuSetty commented 4 years ago

Could you perhaps check if the R installation on the path picked up by python is correct. The best way to ensure this is to set the R_HOME bash environment variable. You can also do this within your Jupiter notebook use %env R_HOME=<path_to_R>

In our initial testing, pygam did not give us the most stable results. But we will add an option to us pygam as a fallback if R gam is not available.

zmokhtari commented 4 years ago

Thank you very much for your help. The issue is resolved.