TIGIT dysfunction role in CD19 CAR-T therapy for NHL

This GitHub contains the source codes analyzed the dataset (the figures and tables to reproduce) used in Jackson & Hong et. al., "Sequential single-cell transcriptional and protein marker profiling reveals TIGIT as a marker of CD19 CAR-T cell dysfunction in patients with non-Hodgkin’s lymphoma", Cancer Discov candisc.1586.2021
Publication URL : https://doi.org/10.1158/2159-8290.CD-21-1586
scRNA-Seq multiplexed raw FASTQs are available at https://ega-archive.org/studies/EGAS00001005356
Refer to workflow.md that R script files used to generate the figures and tables in the paper step by step

Name		Name	Last commit message	Last commit date
Latest commit History 22 Commits
data		data
lib		lib
README.md		README.md
m00_ega_sample_sheet.r		m00_ega_sample_sheet.r
m01_R_module_setup.r		m01_R_module_setup.r
m02a_cellranger_to_seurat.r		m02a_cellranger_to_seurat.r
m03a_qc_cells.r		m03a_qc_cells.r
m04a_cell_id_by_singler.r		m04a_cell_id_by_singler.r
m05a_harmony_findmarkers.r		m05a_harmony_findmarkers.r
m06a_vcluster_heatmap.r		m06a_vcluster_heatmap.r
m07a_celltype_spiderweb.r		m07a_celltype_spiderweb.r
m08a_tigit_expr_by_tgroup.r		m08a_tigit_expr_by_tgroup.r
m09_deg_pre_vs_post_inf.r		m09_deg_pre_vs_post_inf.r
m10_deg_by_cluster_inter.r		m10_deg_by_cluster_inter.r
m11_violin_ridge_gexpr.r		m11_violin_ridge_gexpr.r
m12_dyfscore_TIGIT_on_tsne.r		m12_dyfscore_TIGIT_on_tsne.r
m13_tigitON_pre_vs_post.r		m13_tigitON_pre_vs_post.r
runme.sh		runme.sh
tumor_size_by_bioluminescence.r		tumor_size_by_bioluminescence.r
workflow.md		workflow.md

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