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ManchesterBioinference / GPcounts

Gaussian process regression package for counts data with negative binomial and zero-inflated negative binomial likelihoods
Apache License 2.0
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Looking for a compatible dependency package version list #17

Open vitkl opened 6 months ago

vitkl commented 6 months ago

Hi @sokratiag

I tried following the installation instructions in a clean conda environment but ran into compatibility issues with both default and paper-specific dependency lists. I am looking for a list of compatible dependency packages - would you happen to have a recipe that installs everything necessary, ideally including Scanpy?

sokratiag commented 6 months ago

Hi @vitkl,

Thanks for contacting us. II will look into it and let you know.

NuhaSaud commented 6 months ago

Hi @vitkl, I have updated GPcounts to be compatible with the latest versions of tensorflow and gpflow and tested it with python 3.11. Note that I restructured the code where I moved the functions related to GP in GP_NB_ZINB file and the functions related to RNA-seq analysis in rna_seq_gp file. Please let me know if you face any issues. Thank you for using GPcounts.