TCR-DeepInsight Reference Datasets

Reference single-cell TCR immune profiling datasets for the TCR-DeepInsight analysis.

human_gex_reference_v2.h5ad: Processed H5AD file for transcriptome features from the single-cell TCR immune profiling datasets. anndata.read_h5ad

human_tcr_reference_v2.h5ad: Processed H5AD file for unique TCR clonotypes single-cell TCR immune profiling dataset. anndata.read_h5ad

Yi_2023_Ankylosing_Spondylitis.h5ad: Processed H5AD file from Yi et al., 2023 (GSE216885). anndata.read_h5ad

GSE272993_cd8_nn_labeled_FINAL.fl_tcr.match_v2_5.transfered.h5ad: Processed H5AD file from Wang et al., 2024 (GSE272993). anndata.read_h5ad

human_bulk_tcr_reference.parquet: PARQUET file for bulk TCRβ sequencing. pandas.read_parquet

human_bulk_tcr_reference.cd4.parquet: PARQUET file for bulk TCRβ sequencing for CD4-sorted T cellshuman_bulk_tcr_reference.mait.parquet: PARQUET file for bulk TCRβ sequencing for MAIT cellshuman_bulk_tcr_reference.treg.parquet: PARQUET file for bulk TCRβ sequencing for Treg cellshuman_bulk_tcr_reference.cd8.parquet: PARQUET file for bulk TCRβ sequencing for CD8-sorted T cells

Yi_2023_Ankylosing_Spondylitis.h5ad. anndata.read_h5adProcessed dataset from K. Yi et al. Analysis of Single‐Cell Transcriptome and Surface Protein Expression in Ankylosing Spondylitis Identifies OX40 ‐Positive and Glucocorticoid‐Induced Tumor Necrosis Factor Receptor–Positive Pathogenic Th17 Cells. Arthritis & Rheumatology 75, 1176–1186 (2023).

GSE272993_cd8_nn_labeled_FINAL.fl_tcr.match_v2_5.transfered.h5ad. anndata.read_h5adProcessed dataset from K. Wang et al. Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8+ T cells. Cancer Cell, S1535610824003064 (2024).

human_gex_reference_v2.scatlasvae.ckpt: pretrained weight state dict from scAtlasVAE model for human_gex_reference_v2.h5ad. torch.load

human_bert_pseudosequence.tcr_v2.ckpt: pretrained weight state dict from BERT for human_tcr_reference_v2.h5ad. torch.load

human_bert_pseudosequence_pca.tcr_v2.pkl: pretrained PCA weight for human_tcr_reference_v2.h5ad. pickle.load