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snap-stanford / mars

Discovering novel cell types across heterogenous single-cell experiments
MIT License
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NameError: name 'anndata' is not defined #7

Closed Yale73 closed 3 years ago

Yale73 commented 3 years ago

Hi MARS team,

I got my loom object from seurat object. But when I run the "anndata.read_loom", I got the following error:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-62-f16757897d08> in <module>
----> 1 adata = anndata.read_loom('~/Skin.loom', sparse=True, cleanup=False, X_name='spliced', obs_names='CellID', obsm_names=None, var_names='Gene', varm_names=None, dtype='float32', **kwargs)

**NameError: name 'anndata' is not defined**

Can you help me fix it?

Thanks a bunch! Yale

Yale73 commented 3 years ago

I am sure I have installed the anndata

image

mbrbic commented 3 years ago

You need to import anndata and install loompy. This is completely unrelated to MARS paper and code, please do not use issues to ask general questions. Closing the thread.