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aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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How to define "atac_anndata" in the toturial ?? #97

Closed bitcometz closed 1 year ago

bitcometz commented 1 year ago

hello, thanks for this great tool !!! I try to learn this tool by the toturial. However, I cannot run this step, since the var "atac_anndata" only appear once:

from pycisTopic.label_transfer import *
label_dict = label_transfer(rna_anndata,
                  atac_anndata,
                  labels_to_transfer = ['Seurat_cell_type'],
                  variable_genes = True,
                  methods = ['ingest', 'harmony', 'bbknn', 'scanorama', 'cca'],
                  return_label_weights = False,
                  _temp_dir= tmpDir + 'ray_spill')

Could you please tell how to define it ?

Thanks !!!!