Tutorial

Contents

• Training T cell receptor alpha and beta chains (TCRαβ) seqeunce by BERT
  • Load the reference dataset
  • Training the TCR sequence by BERT
  • Obtaining TCR sequence embedding
• Training Gene Expression (GEX) data by VAE
  • Load the reference dataset
  • Construct and train the GEX model
  • Extract the GEX embedding and Save the trained model
  • Clustering and UMAP visualization
• Clustering TCRαβ and GEX
  • Load the reference dataset
  • Searching for cGxTr clusters without any constraints
  • Searching for cGxTr clusters with at least one common HLA alleles
  • Searching for cGxTr clusters with unique disease type
  • Searching for cGxTr clusters with constrains on TCRs
  • Combining the clustering constrains

Processing 10x Immune Profiling Data

please refer to scAtlasVAE documentation for the tutorial on processing 10x immune profiling data.

TCR Tutorial

Please refer to Training T cell receptor alpha and beta chains (TCRαβ) seqeunce by BERT for the tutorial on TCR training and embedding generation.

GEX Tutorial

Please refer to Training Gene Expression (GEX) data by VAE for the tutorial on GEX training and embedding generation.

TrGx Clustering Tutorial

Please refer to Clustering TCRαβ and GEX for the tutorial on clustering of TCR and GEX embeddings.