Documentation.txt
LICENSE
Make_Docs
README.md
_config.yml
requirements.txt
run.sh
setup.py
Data/10x_Data/Data_Regression.csv
Data/Dash_Human/BMLF/BMLF.tsv
Data/Dash_Human/M1/M1.tsv
Data/Dash_Human/pp65/pp65.tsv
Data/Dash_Murine/F2/F2.tsv
Data/Dash_Murine/M38/M38.tsv
Data/Dash_Murine/M45/M45.tsv
Data/Dash_Murine/NP/NP.tsv
Data/Dash_Murine/PA/PA.tsv
Data/Dash_Murine/PB1/PB1.tsv
Data/Dash_Murine/m139/m139.tsv
Data/Glanville/CTELKLSDY/CTELKLSDY.tsv
Data/Glanville/GILGFVFTL/GILGFVFTL.tsv
Data/Glanville/GLCTLVAML/GLCTLVAML.tsv
Data/Glanville/LPRRSGAAGA/LPRRSGAAGA.tsv
Data/Glanville/NLVPMVATV/NLVPMVATV.tsv
Data/Glanville/TPRVTGGGAM/TPRVTGGGAM.tsv
Data/Glanville/VTEHDTLLY/VTEHDTLLY.tsv
Data/Human_Antigens/A1-CTELKLSDY/A1-CTELKLSDY.tsv
Data/Human_Antigens/A1-VTEHDTLLY/A1-VTEHDTLLY.tsv
Data/Human_Antigens/A2-GILGFVFTL/A2-GILGFVFTL-Dash.tsv
Data/Human_Antigens/A2-GILGFVFTL/A2-GILGFVFTL_Glanville.tsv
Data/Human_Antigens/A2-GLCTLVAML/A2-GLCTLVAML-Dash.tsv
Data/Human_Antigens/A2-GLCTLVAML/A2-GLCTLVAML-Glanville.tsv
Data/Human_Antigens/A2-NLVPMVATV/A2-NLVPMVATV-Dash.tsv
Data/Human_Antigens/A2-NLVPMVATV/A2-NLVPMVATV-Glanville.tsv
Data/Human_Antigens/B7-LPRRSGAAGA/B7-LPRRSGAAGA.tsv
Data/Human_Antigens/B7-TPRVTGGGAM/B7-TPRVTGGGAM.tsv
Data/Murine_Antigens/Db-F2/Db-F2.tsv
Data/Murine_Antigens/Db-M45/Db-M45.tsv
Data/Murine_Antigens/Db-NP/Db-NP.tsv
Data/Murine_Antigens/Db-PA/Db-PA.tsv
Data/Murine_Antigens/Db-PB1/Db-PB1.tsv
Data/Murine_Antigens/Kb-M38/Kb-M38.tsv
Data/Murine_Antigens/Kb-SIY/Kb-1_Sp_Con_SIY.tsv
Data/Murine_Antigens/Kb-SIY/Kb-4_Sp_T_SIYI.tsv
Data/Murine_Antigens/Kb-SIY/Kb-5_TILS_SIY.tsv
Data/Murine_Antigens/Kb-SIY/Kb-6_dLN_SIY.tsv
Data/Murine_Antigens/Kb-TRP2/Kb-2_Sp_Con_TRP2.tsv
Data/Murine_Antigens/Kb-TRP2/Kb-3_Sp_T_TRP2.tsv
Data/Murine_Antigens/Kb-TRP2/Kb-7_dLN_TRP2.tsv
Data/Murine_Antigens/Kb-m139/Kb-m139.tsv
Data/Rudqvist/9H10/9H10-1.tsv
Data/Rudqvist/9H10/9H10-2.tsv
Data/Rudqvist/9H10/9H10-3.tsv
Data/Rudqvist/9H10/9H10-4.tsv
Data/Rudqvist/9H10/9H10-5.tsv
Data/Rudqvist/Combo/RT+9H10-1.tsv
Data/Rudqvist/Combo/RT+9H10-2.tsv
Data/Rudqvist/Combo/RT+9H10-3.tsv
Data/Rudqvist/Combo/RT+9H10-4.tsv
Data/Rudqvist/Combo/RT+9H10-5.tsv
Data/Rudqvist/Control/CONTROL-1.tsv
Data/Rudqvist/Control/CONTROL-2.tsv
Data/Rudqvist/Control/CONTROL-3.tsv
Data/Rudqvist/Control/CONTROL-4.tsv
Data/Rudqvist/Control/CONTROL-5.tsv
Data/Rudqvist/RT/RT-1.tsv
Data/Rudqvist/RT/RT-2.tsv
Data/Rudqvist/RT/RT-3.tsv
Data/Rudqvist/RT/RT-4.tsv
Data/Rudqvist/RT/RT-5.tsv
Data/Sidhom/SIY/1_Sp_Con_SIY.tsv
Data/Sidhom/SIY/4_Sp_T_SIYI.tsv
Data/Sidhom/SIY/5_TILS_SIY.tsv
Data/Sidhom/SIY/6_dLN_SIY.tsv
Data/Sidhom/TRP2/2_Sp_Con_TRP2.tsv
Data/Sidhom/TRP2/3_Sp_T_TRP2.tsv
Data/Sidhom/TRP2/7_dLN_TRP2.tsv
Data/Zhang/ATP6AP1-KLG_G3W/Neg_ATP6AP1-KLG_G3W/Neg_ATP6AP1-KLG_G3W.tsv
Data/Zhang/ATP6AP1-KLG_G3W/Pos_ATP6AP1-KLG_G3W/Pos_ATP6AP1-KLG_G3W.tsv
Data/Zhang/GNL3L-R4C/Neg_GNL3L-R4C/Neg_GNL3L-R4C.tsv
Data/Zhang/GNL3L-R4C/Pos_GNL3L-R4C/Pos_GNL3L-R4C.tsv
Data/Zhang/MART1-A2L/Neg_MART1-A2L/Neg_MART1-A2L.tsv
Data/Zhang/MART1-A2L/Pos_MART1-A2L/PosMART1-A2L.tsv
Data/Zhang/YFV-LLW/Neg_YFV-LLW/Neg_YFV-LLW.tsv
Data/Zhang/YFV-LLW/Pos_YFV-LLW/PosYFV-LLW.tsv
DeepTCR/DeepTCR.py
DeepTCR/__init__.py
DeepTCR.egg-info/PKG-INFO
DeepTCR.egg-info/SOURCES.txt
DeepTCR.egg-info/dependency_links.txt
DeepTCR.egg-info/top_level.txt
DeepTCR/functions/Layers.py
DeepTCR/functions/MIL.py
DeepTCR/functions/__init__.py
DeepTCR/functions/data_processing.py
DeepTCR/functions/utils_s.py
DeepTCR/functions/utils_u.py
DeepTCR_old/DeepTCR.py
DeepTCR_old/__init__.py
DeepTCR_old/functions/Layers.py
DeepTCR_old/functions/MIL.py
DeepTCR_old/functions/__init__.py
DeepTCR_old/functions/data_processing.py
DeepTCR_old/functions/utils_s.py
DeepTCR_old/functions/utils_u.py
ancillary_analysis/phenograph_local/__init__.py
ancillary_analysis/phenograph_local/bruteforce_nn.py
ancillary_analysis/phenograph_local/classify.py
ancillary_analysis/phenograph_local/cluster.py
ancillary_analysis/phenograph_local/core.py
ancillary_analysis/phenograph_local/louvain/community
ancillary_analysis/phenograph_local/louvain/community.exe
ancillary_analysis/phenograph_local/louvain/convert
ancillary_analysis/phenograph_local/louvain/convert.exe
ancillary_analysis/phenograph_local/louvain/hierarchy
ancillary_analysis/phenograph_local/louvain/hierarchy.exe
ancillary_analysis/phenograph_local/louvain/linux-community
ancillary_analysis/phenograph_local/louvain/linux-convert
ancillary_analysis/phenograph_local/louvain/linux-hierarchy
ancillary_analysis/phenograph_local/louvain/louvain-readme.txt
ancillary_analysis/phenograph_local/louvain/phenograph-readme.txt
ancillary_analysis/supervised/BM_Analysis.py
ancillary_analysis/supervised/CM038_Qualitative_U.py
ancillary_analysis/supervised/DeepTCR_v_SVM.py
ancillary_analysis/supervised/Model_Info.py
ancillary_analysis/supervised/NN_Assessment_utils.py
ancillary_analysis/supervised/Regression.py
ancillary_analysis/supervised/Sup_Human_HLA.py
ancillary_analysis/supervised/Sup_Human_TCR.py
ancillary_analysis/supervised/Sup_Human_TCR_HLA.py
ancillary_analysis/supervised/Sup_Motifs.py
ancillary_analysis/supervised/Sup_Rep_Human_Certainty.py
ancillary_analysis/supervised/Sup_Seq_ROC.py
ancillary_analysis/supervised/Supervised_Repertoire_Human.py
ancillary_analysis/supervised/Supervised_Repertoire_Murine.py
ancillary_analysis/supervised/alpha_v_beta.py
ancillary_analysis/supervised/alpha_v_beta_rep_seq.py
ancillary_analysis/supervised/sup_v_unsup.py
ancillary_analysis/supervised/tc_type.py
ancillary_analysis/unsupervised/GLIPH.csv
ancillary_analysis/unsupervised/Gliph_v_Hamming.py
ancillary_analysis/unsupervised/Human_Antigens.py
ancillary_analysis/unsupervised/Murine_Antigens.py
ancillary_analysis/unsupervised/NN_Assessment_utils.py
ancillary_analysis/unsupervised/Rep_Dendrogram.py
ancillary_analysis/unsupervised/Repertoire_Classification.py
ancillary_analysis/unsupervised/Rudqvist_Length.py
ancillary_analysis/unsupervised/Run_Gliph.py
ancillary_analysis/unsupervised/Structural_Diversity_Benchmark.py
tutorials/1 - Loading Data.ipynb
tutorials/supervised/1 - Supervised Sequence Classification.ipynb
tutorials/supervised/2 - Supervised Repertoire Classification.ipynb
tutorials/unsupervised/1 - Training VAE.ipynb
tutorials/unsupervised/2 - Clustering TCRSeq Data.ipynb
tutorials/unsupervised/3 - Sequence & Repertoire Level Heatmaps.ipynb
tutorials/unsupervised/4 - Structural Diversity Assessment.ipynb
tutorials/unsupervised/5 - Visualization of Results.ipynb
tutorials/unsupervised/6 - KNN Classification.ipynb
tutorials/unsupervised/7 - Motif Identification.ipynb