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Figure 1

  • B-C Analysis/TCAT/F2_PlotcGEPs_Latest.ipynb
  • D Analysis/TCAT/F2D_S2_Marker_Gene_Plot_Latest.ipynb

Figure 2

  • A-C Analysis/PerDataset/Sparks/PredictLineage_Usage_vs_Clusters_ROC_latest.ipynb
  • D Analysis/TCAT/Polarization_MarkerHeatmaps.ipynb

Figure 3

  • A-C Analysis/TCAT/Cluster_Heterogeneity_COMBAT_Latest.ipynb
  • D Analysis/TCAT/Proliferation_Lineages_Latest.ipynb
  • E Analysis/TCAT/Polarization_Vs_Pop_MC_latest.ipynb

Figure 4

  • A,C,D Analysis/PerDataset/Aimseq/Make_UMAP_Plots_Latest.ipynb
  • E,F Analysis/PerDataset/Aimseq/TCAT_Stimseq_Latest.ipynb

Figure 5

  • A-D Analysis/TCAT/Activation_Prediction/Activation_Prediction_Results_Latest.ipynb
  • E,H Analysis/TCAT/Activation_Prediction/Activation_Proliferation_Analysis_Latest.ipynb
  • F Analysis/TCAT/Activation_Prediction/TCR_vs_Activation.ipynb
  • G,I-K Analysis/TCAT/Activation_Prediction/Activation_Phenotype_Analysis_Latest.ipynb

Figure 6

  • A-B Analysis/Revision/Melanoma_Outcome/analyze_melanoma_outcome.ipynb
  • C Analysis/Revision/CRC_Outcome/analyze_crc.ipynb
  • D Analysis/Revision/BCC_Outcome/Analyze_YostEtAl_BCCandSCC.ipynb
  • E-G Analysis/Revision/ICI_Prediction.ipynb

S1

  • A-E Analysis/TCAT/Simulation_Benchmark/Test_Simulated_Usage_20241101.ipynb
  • F Analysis/TCAT/Dataset_Stats.ipynb
  • G Analysis/TCAT/S1B_Matched_GEPs_PerDataset_Latest.ipynb
  • H Analysis/TCAT/S1C_Correlate_PCA_Latest.ipynb

S2

  • A Analysis/TCAT/F2_PlotcGEPs_Latest.ipynb
  • B-C Analysis/PerDataset/COMBAT/Manually_Gate_Lineages_Latest.ipynb
  • D-E Analysis/TCAT/Associate_Usage_CellQuality_Latest.ipynb
  • F Analysis/PerDataset/AMPRA/Count_Intergenic.ipynb
  • G Analysis/TCAT/Compare_IEG_Usage_AllPBMCLineages_Latest.ipynb

S3

  • A Analysis/PerDataset/Sparks/Manually_Gate_Lineages_Latest.ipynb
  • B Analysis/TCAT/Benchmarking_Latest.ipynb
  • C Analysis/PerDataset/Sparks/PredictLineage_Usage_vs_Clusters_ROC_latest.ipynb
  • D Analysis/PerDataset/Sparks/ValidateFunctionalGEPs_Latest.ipynb
  • E Analysis/TCAT/Cytotoxic_MarkerHeatmaps.ipynb

S4

  • A Analysis/TCAT/Proliferation_Lineages_Latest.ipynb
  • B-C Analysis/TCAT/Cluster_Heterogeneity_COMBAT_Latest.ipynb
  • D Analysis/TCAT/Cytotoxic_MarkerHeatmaps.ipynb
  • E Analysis/TCAT/Polarization_Vs_Pop_MC_latest.ipynb
  • F Analysis/TCAT/Polarization_MarkerHeatmaps.ipynb

S5

  • C-E Analysis/PerDataset/Aimseq/Make_ADT_Association_Plot_Latest.ipynb
  • F Analysis/PerDataset/Aimseq/Manually_Gate_Lineages_Stimseq_Latest.ipynb
  • G Analysis/PerDataset/Aimseq/TCAT_Stimseq_Latest.ipynb
  • H Analysis/TCAT/ProliferationGEP_Associations_Latest.ipynb

S6

  • A Analysis/PerDataset/COMBAT/DefineActivation_MAGIC.ipynb
  • B Analysis/TCAT/Activation_Prediction/S9_ActivationFeatureSelection.ipynb
  • C-E Analysis/TCAT/Activation_Prediction/Activation_Prediction_Results_Latest.ipynb
  • F-G Analysis/TCAT/Benchmarking_Latest.ipynb
  • H Analysis/TCAT/Activation_Prediction/Activation_Proliferation_Analysis_Latest.ipynb
  • I Analysis/TCAT/Activation_Prediction/TCR_vs_Activation.ipynb
  • J-K Analysis/TCAT/Activation_Prediction/Activation_Phenotype_Analysis_Latest.ipynb

S7

  • A-F Analysis/TCAT/Phenotype_Associations_Latest.ipynb

S8

  • A,B,C,I Analysis/Revision/Melanoma_Outcome/analyze_melanoma_outcome.ipynb
  • D,K Analysis/Revision/BCC_Outcome/Analyze_YostEtAl_BCCandSCC.ipynb
  • E,F,J Analysis/Revision/CRC_Outcome/analyze_crc.ipynb
  • G-H Analysis/Revision/ICI_Prediction.ipynb

Extended Data

  • 1 ????
  • 2A Analysis/PerDataset/AMPRA/cNMF_BatchCorrect_Latest.ipynb
  • 2B Analysis/PerDataset/HaoEtAl/cNMF_BatchCorrect_allT_useRNA_Latest.ipynb
  • 2C Analysis/PerDataset/COMBAT/cNMF_BatchCorrect_Latest.ipynb
  • 2D Analysis/PerDataset/UKCOVID/cNMF_BatchCorrect_Latest.ipynb
  • 2E Analysis/PerDataset/XTissueImmuneAtlas/cNMF_BatchCorrect_NoBlood_XTissue_Latest.ipynb
  • 2F Analysis/PerDataset/Pancancer/cNMF_BatchCorrect_NoBlood_PanCancer_Latest.ipynb
  • 2G Analysis/PerDataset/TBRU/cNMF_BatchCorrect_Latest.ipynb
  • 3 Analysis/TCAT/F2D_S2_Marker_Gene_Plot_Latest.ipynb
  • 4 Analysis/TCAT/Compare_IEG_Usage_AllPBMCLineages_Latest.ipynb
  • 5A-B Analysis/PerDataset/Sparks/PredictLineage_Usage_vs_Clusters_ROC_latest.ipynb
  • 6A ????
  • 6B-E Analysis/PerDataset/TCAT/Cluster_Heterogeneity_COMBAT_Latest.ipynb
  • 7B Analysis/PerDataset/Aimseq/TCAT_Stimseq_Latest.ipynb
  • 7C-D Analysis/TCAT/Activation_Prediction/Activation_by_Dataset.ipynb
  • 7E Analysis/TCAT/ProliferationGEP_Associations_Latest.ipynb
  • 8A Analysis/TCAT/Activation_Prediction/Activation_Prediction_Results_Latest.ipynb
  • 8B-C Analysis/TCAT/Benchmarking_Latest.ipynb
  • 8D-F Analysis/TCAT/Activation_Prediction/Activation_Phenotype_Analysis_Latest.ipynb
  • 9A Analysis/TCAT/Activation_Prediction/Activation_by_Dataset.ipynb
  • 9B Analysis/TCAT/Activation_Prediction/Activation_Phenotype_Analysis_Latest.ipynb
  • 9C Analysis/TCAT/Phenotype_Associations_Latest.ipynb
  • 9D-E Analysis/TCAT/PerDataset/Pancancer/Tph_Bcell.ipynb
  • 10A-C Analysis/Revision/CRC_Outcome/analyze_crc.ipynb
  • 10A-C Analysis/Revision/BCC_Outcome/Analyze_YostEtAl_BCCandSCC.ipynb
  • 10A-C Analysis/Revision/Melanoma_Outcome/analyze_melanoma_outcome.ipynb