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rajewsky-lab / novosparc

BSD 3-Clause "New" or "Revised" License
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Question about implementation and input data #48

Open s849 opened 3 years ago

s849 commented 3 years ago

Hello,

Thanks for developing novosparc. I have a couple of questions;

1. I am first trying to run the example data - I am coming up with this error after I run the following line: tissue_with_markers = novosparc.cm.Tissue(dataset=dataset.raw.to_adata(), locations=locations, atlas_matrix=atlas_matrix)

TypeError Traceback (most recent call last)

in ----> 1 tissue_with_markers = novosparc.cm.Tissue(dataset=dataset.raw.to_adata(), locations=locations, atlas_matrix=atlas_matrix) TypeError: __init__() got an unexpected keyword argument 'atlas_matrix' Any ideas what the error might be? **2.** What is deg.txt file? Is this the matrix of the reference marker genes? **3.** Do I need to include digitized images of the expression patterns of reference marker genes? If so, do all digitized images need to match the reference marker genes? OR, just including the reference marker genes suffice? Thank you very much for your help!