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scbean's Issues

tfl.findNeighbors[adata_integrate] gives: KeyError: 'distances'

Hi!
I was following the tutorial for integrating scRNA-seq data and scATAC-seq data using the dataset provided. However, I get the following error when I run the step: atac = tfl.findNeighbors(adata_integrate)

KeyError Traceback (most recent call last)
Cell In[21], line 1
----> 1 atac=tfl.findNeighbors(adata_integrate)

File ~/anaconda3/envs/scbean/lib/python3.8/site-packages/scbean/tools/transferLabel.py:23, in findNeighbors(adata)
21 ann_atac["pred_max_score"]=0.0
22 querycells = ann[ann['tech']=="atac"]['nid']
---> 23 dist=adata.uns['neighbors']['distances']
24 weights[weights.index]=np.ones(len(weights))
25 weights["Platelets"]=0.001

KeyError: 'distances'

Any help would be greatly appreciated!

ModuleNotFoundError: No module named 'fastlmm.util.stats.quadform'

Thanks for sharing the excellent work! However, I faced an issue while running vimcca. Do you have any suggestions about this error? Thanks!!

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_3609060/839549067.py in <module>
      1 import scanpy as sc
----> 2 from scbean.model import vimcca

~/anaconda3/envs/environment_deepmerge/lib/python3.7/site-packages/scbean/__init__.py in <module>
      1 from __future__ import absolute_import
      2 __all__ = ['model', 'tools']
----> 3 from . import model
      4 from . import tools

~/anaconda3/envs/environment_deepmerge/lib/python3.7/site-packages/scbean/model/__init__.py in <module>
      1 from .vipcca import VAE, CVAE, CVAE2, CVAE3
      2 from .davae import fit_integration, DAVAE, DACVAE
----> 3 from .visgp import VISGP
      4 from .vimcca import VIMCCA, fit_integration
      5 

~/anaconda3/envs/environment_deepmerge/lib/python3.7/site-packages/scbean/model/visgp.py in <module>
      5 import multiprocessing
      6 from tqdm import tqdm
----> 7 import fastlmm.util.stats.quadform as qf
      8 os.environ['TF_CPP_MIN_LOG_LEVEL'] = "3"
      9 import tensorflow as tf

ModuleNotFoundError: No module named 'fastlmm.util.stats.quadform'

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