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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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Hello everyone, I am having issues running sceasy for conversion from sce object to anndata. Following repo instructions, I run: #72

Open Pancreaticpathway opened 1 year ago

Pancreaticpathway commented 1 year ago

Hello everyone, I am having issues running sceasy for conversion from sce object to anndata. Following repo instructions, I run: library(sceasy) loompy <- reticulate::import('loompy') and got: Error in py_module_import(module, convert = convert) : ImportError: cannot import name 'get_loom_spec_version' from 'loompy.utils'

cathalgking commented 1 year ago

I am having a similar issue in converting a SPE (10x visium Spatial experiment) to anndata:

I have the anndata library called with library(anndata)

sceasy::convertFormat(C1_sce, from="sce", to="anndata", outFile='/PATH/C1_sce_test.h5ad') Error: ModuleNotFoundError: No module named 'anndata' In addition: Warning message: In .regularise_df(as.data.frame(SummarizedExperiment::colData(obj)), : Dropping single category variables:in_tissue, sample_id