Liana R vs Liana py versions

[KyriakisDimitrios]

Hello, Thank you very much for this amazing tool. I would like to know if the recent Liana_R version 0.1.11 means Liana_py v 0.1.11 or Liana_R v0.1.11 == Liana_py v1.0.3 Thanks

[dbdimitrov]

Hi Dimitrios,

There is no connection of the versions between python and R. Though, the single-cell component of Liana-py is of course highly consistent with the latest version in R. We essentially show a correlation between the two of 0.98 here: https://ccc-protocols.readthedocs.io/en/latest/notebooks/ccc_R/S3_Score_Consistency.html#Comparison-with-Python-output:

Eventually, our plan is to transition the backend of the R package to the more efficient (and now more comprehensive) python package. Essentially, to call liana-py via liana-R :)

Hope this helps.

Daniel

[KyriakisDimitrios]

Thanks! One more question about the R version. The rank_aggregate does not have the arguments like the python version has. Is it running with the default hyperparams of python ? e.g expr_prop=0.1, min_cells=5, n_perms=1000,

I tried to find the parameters in the github but I did not manage

Thanks again

[dbdimitrov]

In R, these parameters are passed to liana_wrap and rank_aggregate only aggregates the results from different methods. In Python rank aggregate does both.