How to use Leiden clustering with Seurat? #7

lm687 · 2024-07-05T10:04:23Z

Using reticulate - Carla, can we get the solution here? We had a minimal example. thanks

liezeltamon · 2024-07-05T10:08:30Z

This is what I do and it works also even when using renv:

reticulate R package will be used to load leidenalg python module and dependencies numpy and pandas

mamba create -n leiden leidenalg numpy pandas

Set RETICULATE_PYTHON in .Renviron to path of python environment with the packages for reticulate to find. For example:

RETICULATE_PYTHON=/project/sims-lab/ltamon/mamba_installation/conda/envs/leiden/bin/python

library(reticulate)
reticulate::import("numpy")
reticulate::import("pandas")
reticulate::import("leidenalg")

kevinrue · 2024-07-05T10:09:07Z

Happy to explain more if needed

lm687 added Seurat Seurat - R package for single cell R R programming language labels Jul 5, 2024

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