TCR_usages

Collection of scripts associated with correlating HLA genotypes with TCR usages

Name		Name	Last commit message	Last commit date
BLAST_to_FamilyCounts.ipynb		BLAST_to_FamilyCounts.ipynb
DGN_AminoAcids_OLS.ipynb		DGN_AminoAcids_OLS.ipynb
DGN_Analyses.ipynb		DGN_Analyses.ipynb
DGN_BLAST_to_FamilyCounts.ipynb		DGN_BLAST_to_FamilyCounts.ipynb
DGN_Construct_BLAST_and_SLURM.ipynb		DGN_Construct_BLAST_and_SLURM.ipynb
DGN_Families_OLS.ipynb		DGN_Families_OLS.ipynb
DGN_Get_HLA_df.ipynb		DGN_Get_HLA_df.ipynb
DGN_Get_VDJ_usage_df.ipynb		DGN_Get_VDJ_usage_df.ipynb
DGN_Get_VDJ_usage_df_collapsed.ipynb		DGN_Get_VDJ_usage_df_collapsed.ipynb
DGN_Pseudogenes.ipynb		DGN_Pseudogenes.ipynb
DGN_Sharon_Compute_Usage_Plotting.ipynb		DGN_Sharon_Compute_Usage_Plotting.ipynb
DGN_Sharon_TargSeq_Combined_Analyses.ipynb		DGN_Sharon_TargSeq_Combined_Analyses.ipynb
DGN_TranscriptCounts_FamilyCounts_AminoAcidCounts.ipynb		DGN_TranscriptCounts_FamilyCounts_AminoAcidCounts.ipynb
DGN_VDJ_OLS_LOOP.ipynb		DGN_VDJ_OLS_LOOP.ipynb
DGN_X_matrices Amino Acids.ipynb		DGN_X_matrices Amino Acids.ipynb
DGN_eQTL.ipynb		DGN_eQTL.ipynb
HLA_alleles.ipynb		HLA_alleles.ipynb
J24Seq.ipynb		J24Seq.ipynb
KIR BLAST.ipynb		KIR BLAST.ipynb
Liblau_VDJComputeUsage.ipynb		Liblau_VDJComputeUsage.ipynb
MultiPlotting-Copy1.ipynb		MultiPlotting-Copy1.ipynb
MultiPlotting.ipynb		MultiPlotting.ipynb
MultiSeqPreprocess.ipynb		MultiSeqPreprocess.ipynb
PCA.ipynb		PCA.ipynb
Plotting.ipynb		Plotting.ipynb
README.md		README.md
Related_People.ipynb		Related_People.ipynb
TargetedSequencing_Analyses.ipynb		TargetedSequencing_Analyses.ipynb
TargetedSequencing_DataMatrices-Copy1.ipynb		TargetedSequencing_DataMatrices-Copy1.ipynb
TargetedSequencing_DataMatrices.ipynb		TargetedSequencing_DataMatrices.ipynb
VDJCorrelateHLA.ipynb		VDJCorrelateHLA.ipynb
rs1154155 eQTL J24 J28.ipynb		rs1154155 eQTL J24 J28.ipynb

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