├── .gitignore ├── LICENSE ├── README.md ├── data ├── category_colors.json ├── cite-seq_cat_colors.json ├── citeseq-dashboard │ ├── category_colors.json │ ├── merge_data.parquet │ ├── merge_viz.json │ └── meta_cell.parquet ├── citeseq_adt_merge.txt ├── citeseq_adt_pbmc.txt ├── citeseq_adt_plaque.txt ├── citeseq_gex_pbmc-and-plaque.txt ├── citeseq_gex_pbmc.txt ├── citeseq_gex_plaque.txt ├── citeseq_gex_plaque_cd4_t_cells.txt ├── citeseq_gex_plaque_cd8_t_cells.txt ├── citeseq_gex_plaque_macrophages.txt ├── citeseq_gex_plaque_t_cells.txt ├── cluster-colors.json ├── lig-rec_sym-asym_fold_change_btwn_CD4-CD4.txt ├── lig-rec_sym-asym_fold_change_btwn_CD4-CD8.txt ├── lig-rec_sym-asym_fold_change_btwn_CD4-Mac.txt ├── lig-rec_sym-asym_fold_change_btwn_CD8-CD4.txt ├── lig-rec_sym-asym_fold_change_btwn_CD8-CD8.txt ├── lig-rec_sym-asym_fold_change_btwn_CD8-Mac.txt ├── lig-rec_sym-asym_fold_change_btwn_Mac-CD4.txt ├── lig-rec_sym-asym_fold_change_btwn_Mac-CD8.txt ├── lig-rec_sym-asym_fold_change_btwn_Mac-Mac.txt ├── meta_cell.parquet ├── scRNA-seq_cohort_cd4_t_cells.txt ├── scRNA-seq_cohort_cd8_t_cells.txt ├── scRNA-seq_cohort_macrophages.txt ├── scRNA-seq_cohort_t_cells.txt └── t_cell_cat_colors.json ├── img ├── citeseq_adt.gif ├── citeseq_adt_pbmc_plaque.png ├── citeseq_gex_cd4_t_cells_plaque.png ├── citeseq_gex_cd8_t_cells_plaque.png ├── citeseq_gex_macrophages_plaque.png ├── citeseq_gex_pbmc_plaque.png ├── citeseq_gex_t_cells_plaque.png ├── lig-rec_sym-asym_diff_interactions.png ├── scrnaseq_cohort_cd4_t_cells.png ├── scrnaseq_cohort_cd8_t_cells.png ├── scrnaseq_cohort_macrophages.png └── scrnaseq_cohort_t_cells.png ├── notebooks ├── 1.0_CITE-seq_ADT_PBMC_and_Plaque.ipynb ├── 1.1_CITE-seq_GEX_PBMC_and_Plaque.ipynb ├── 1.2_CITE-seq_GEX_Plaque_T_Cells.ipynb ├── 1.3_CITE-seq_GEX_Plaque_CD4_T_Cells.ipynb ├── 1.4_CITE-seq_GEX_Plaque_CD8_T_Cells.ipynb ├── 1.5_CITE-seq_GEX_Plaque_Macrophages.ipynb ├── 2.0_scRNA-seq_Cohort_T_Cells.ipynb ├── 2.1_scRNA-seq_Cohort_CD4_T_Cells.ipynb ├── 2.2_scRNA-seq_Cohort_CD8_T_Cells.ipynb ├── 2.3_scRNA-seq_Cohort_Macrophages.ipynb ├── 3.0_Ligand-Receptor_Sym-vs-Asym_Differential_Regulation.ipynb ├── 4.0_Prepare_CITE-seq_Dashboard.ipynb ├── Dashboard_CITE-seq_PBMC_and_Plaque.ipynb ├── Papermill.ipynb ├── helper_functions.py └── himc_helper_functions_v0_17_0.py ├── papermill_notebooks └── 1.0_CITE-seq_ADT_PBMC_and_Plaque.ipynb ├── postBuild ├── reports └── 1.0_CITE-seq_ADT_PBMC_and_Plaque.html └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/giannarelli-lab/Single-Cell-Immune-Profiling-of-Atherosclerotic-Plaques/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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