CellO
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deweylab
CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
Hello everyone. I just installed the latest cello-classify version with pip. Version 2.0.3. Installation went fine. When I try to use it, I get an error. I execute this cell...
Bumps [numpy](https://github.com/numpy/numpy) from 1.17.1 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...
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Bumps [scipy](https://github.com/scipy/scipy) from 1.3.1 to 1.10.0. Release notes Sourced from scipy's releases. SciPy 1.10.0 Release Notes SciPy 1.10.0 is the culmination of 6 months of hard work. It contains many...
Hello all, I run: `pip install pygraphviz leidenalg scanpy cello-classify` And this was what I got: pygraphviz/graphviz_wrap.c:2711:10: fatal error: 'graphviz/cgraph.h' file not found #include "graphviz/cgraph.h" ^~~~~~~~~~~~~~~~~~~ 1 error generated. error:...
Hi, anndata has layers to save more information. I'm wondering if scanpy_cello can support the selection of layers to use. Thus we don't need to save separate object files to...
I receive the error message, ValueError: Unable to determine gene collection. Please make sure the input dataset specifies either HUGO gene symbols or Entrez gene ID's. W1_1.var.head() gene_ids feature_types highly_variable...
Hello and thanks for your amazing tool. I am trying it out right now, but somehow it seems to me that either I don't quite understand how the most specif...
Hi, thank you for developing this useful tool. There are two things I want to report. 1. I encountered an error and found that it was because adata.X were "stored...
if _select_one_most_specific has no prediction and appends '' in https://github.com/deweylab/CellO/blob/7d375810a0d310f3bdafc46a33ce7257860b882d/cello/cello.py#L738-L743 that seems to break https://github.com/deweylab/CellO/blob/7d375810a0d310f3bdafc46a33ce7257860b882d/cello/cello_predict.py#L191-L194 so I add this check and give the label unknown.
Hi, Thank you for developing this very useful tool! We encountered an error while trying to classify our cells with a pre-trained model. The prediction itself seems to work and...
