🧬 ASI-FIMSA Bioinformatics Workshop 1

https://github.com/tuonglab/FIMSA-training-workshop-1

This series introduces basic concepts in single-cell and TCR/BCR analysis using Python. All notebooks are designed to run in Google Colab.

Tutorial 1

Tutorial 2

Tutorial 3

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📚 Notebooks

1. tutorial-1 (scRNA-seq with Scanpy)

• Intro to single-cell data in Python
• AnnData structure (.X, .obs, .var)
• UMAP visualization

Tools: Scanpy

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2. tutorial-2 (TCR Analysis with Dandelion)

• Intro to single-cell TCR sequencing
• Contig annotation files
• AIRR format
• Clonotype network visualization

Tools: Scanpy, Dandelion

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3. tutorial-3 (Deep Learning on TCRs)

• Train a model on TCR sequences (~10k)
• Use a pre-trained model
• Visualize embeddings

Tools: PyTorch

workshop 3 slides

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▶️ How to Use

• Open notebooks in Google Colab
• Run cells from top to bottom

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🎯 Outcomes

By the end, you will:

• Understand DataFrames and AnnData
• Run a basic single-cell workflow
• Explore TCR data
• Apply deep learning to biological sequences

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👥 Contributors

• Norman
• Linlin

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