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wallet-maker merged 1 commit into from
Jul 7, 2026
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Update README to remove outdated tutorial section #29

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4 changes: 0 additions & 4 deletions README.md
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Expand Up @@ -125,10 +125,6 @@ Please refer to our [readthedocs](https://cytopus.readthedocs.io) for more detai
Learn how to explore the Knowledge Base and retrieve a dicitionary which can be used for [Spectra](https://github.com/dpeerlab/spectra):
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/wallet-maker/cytopus/blob/main/notebooks/KnowledgeBase_queries_colaboratory.ipynb)

### Interactive tutorial for Generating a cytopus Knowledge Base object:
Learn how to create a Knowledge Base object from gene sets annotations and cell type hierarchies stored in .csv files:
[here](https://github.com/wallet-maker/cytopus/blob/main/notebooks/KnowledgeBase_construct.ipynb)

### Interactive utils tutorial - Labeling Factor Analysis Outputs (Spectra):
Learn how to label marker genes from factor analysis, determine factor cell type specificity and export the Knowledge Base content as .gmt files for other applications:
[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/wallet-maker/cytopus/blob/main/notebooks/Cytopus_utils_tutorial.ipynb)
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