I have a very complex data set which underwent a couple of preprocessing steps, all in python (e.g. integration using scanvi etc.). From what I found there is no conversion between anndata object and cds yet. So I had to find a work around and export the raw counts + gene names + meta data (anndata observation).
Is there a way to export the pseudotime and the learned graph of monocle and load it back into python? I would like to use my python umap projection for completeness.
This is the best idea I could come up with, if anyone has any other ideas or workarounds how to integrate monocle into an existing python workflow please let me know!
Dear all,
I have a very complex data set which underwent a couple of preprocessing steps, all in python (e.g. integration using scanvi etc.). From what I found there is no conversion between anndata object and cds yet. So I had to find a work around and export the raw counts + gene names + meta data (anndata observation).
Is there a way to export the pseudotime and the learned graph of monocle and load it back into python? I would like to use my python umap projection for completeness.
This is the best idea I could come up with, if anyone has any other ideas or workarounds how to integrate monocle into an existing python workflow please let me know!
Thanks for any help!!