Maria Rosaria Nucera
Maria Rosaria Nucera
> I have the same question! The authors did no normalization (`sc.pp.normalize_total()` and `sc.pp.log1p()`) before proceeding to the GRNBoost2 step in the PBMC tutorial (https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.ipynb), but they did `sc.pp.log1p()` for...
yes I just copied info from the seurat obj like this: (where cds_seur is the output of new_cell_data_set(matrix,cell_metadata = cell_metadata, gene_metadata = gene_annotation)) reducedDim(cds_seur, type = "PCA")
> and by the way; I am trying to use it from Seurat not Scanpy. > > basically as bellow: > ``` > # monocle3 function > gene_annotation = as.data.frame(rownames(my.seurat.obj@assays$RNA@counts))...
Could be some problem with the ray version as I think that ray>=2.3 isn't compatible with pydantic>=2. In general, with pydantic 2.0.3 when I import ray I get: ### import...
I have the same error, just with 'profile_tss', I have no problem with the other metrics. I tried to run it @SeppeDeWinter , here is the output: ### annot Chromosome...
> This issue might be solved now, can you check this out? [aertslab/pycisTopic#81 (comment)](https://github.com/aertslab/pycisTopic/issues/81#issuecomment-1643460879) > > Best, > > Seppe Yes, I followed this and it is fixed for me...
> It seems that my tests never caught any situation requiring to call logging in palette management, I have added the import in the latest commit of `v1.1.2dev`, let me...
Hi @LouisFaure! thank you very much for the explanation. I understood the source of the problem. adata.uns["graph"]["pp_seg"] has one more seg than adata.obs.seg.cat.categories has no cells get assigned to each....