Extracting fragment count matrix
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- Dominant language
- Python
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- 323
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Description
Hello,
Thanks for the great package!
I am trying to extract the fragment count matrix to implement with the following notebook:
https://github.com/aertslab/pycisTopic/blob/old/notebooks/Toy_melanoma-RTD.ipynb
However, I cannot see where to extract the fragment count matrix.
I believe this is stored in adata.obsm['fragment_paired'], but I cannot see how to extract the fragment names.
Thank you for your help
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Research direction
Start with the linked Toy_melanoma-RTD.ipynb notebook and inspect how the fragment count matrix is represented in adata.obsm['fragment_paired']. Determine how fragment names can be retrieved and document the extraction path so the notebook workflow can be reproduced.
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Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics, data
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100