├── .gitignore ├── 1_MT_Coverage ├── 1.1_Compare_MT_coverage.R ├── 1.2_MT_coverage.R └── 1.3_BT142_K562.R ├── 2_Cell_line_mixes_decontX ├── 2.1_SW_CellLineMix_decontX.R └── 2.2_TenX_CellLineMix_decontX.R ├── 3_Cell_line_mixes_variants ├── 3.1_SW_CellLineMix_variants.R ├── 3.2_SW_K562_clones.R ├── 3.3_TenX_CellLineMix_variants.R ├── 3.4_TenX_K562_clones.R ├── SW_CellLineMix_Cells.rds ├── TenX_CellLineMix_Cells.rds └── TenX_CellLineMix_Variants1.txt ├── 4_CH_sample ├── 4.1_MarkerGenes.txt ├── 4.1_Patient10_UMAP.R ├── 4.2_Variant_Selection.R ├── 4.2_vois.txt ├── 4.3_Variants_Of_Interest.R ├── 4.3_vois_order.txt ├── 4.4_LineageBias.R └── 4.4_positive_cells.txt ├── 5_TCR-Seq ├── 5.1_Recluster_TNK.R ├── 5.2_Clonal_overlap.R ├── 5.3_Expression_heatmap.R ├── Duncan_210805 │ ├── 20210805_maester2_TCRalignSortMappingSummary.txt │ ├── 20210805_maester2_vfilter9.csv │ ├── lane2_barcodes.txt │ └── maester2_processing.ipynb └── TNK_MarkerGenes.txt ├── 6_TET2_mutations ├── 6.1_TET2_heatmap.R ├── 6.2_Stats_for_results.R ├── MutationData │ ├── ASXL1.1886.FilteredCells.txt │ ├── ASXL1.1898.FilteredCells.txt │ ├── TET2.2340.FilteredCells.txt │ ├── TET2.3078.FilteredCells.txt │ ├── TET2.3626.FilteredCells.txt │ └── TET2.4104.FilteredCells.txt └── got.txt ├── 7_Slingshot └── 7_Slingshot.R ├── 8_Glioblastoma ├── 8.1_MGH252_variants.txt ├── 8.1_MGH252_voi.R ├── 8.2_Vincent_Caleb_indel.R ├── 8.3_MGH252_2056GA.R ├── Caleb email 211018 │ └── mut13984-glio.xlsx ├── Chadi Slack 210819 │ ├── MGH252_NoM_A_C_PBMC_MetaData.txt │ └── MGH252_NoM_A_C_PBMC_UMAP.txt └── Chadi email 210721 │ ├── MGH252_A_C_PBMC_MetaData.txt │ └── MGH252_A_C_PBMC_UMAP.txt ├── 9_K562_ATAC ├── 9.1_Align_and_deduplicate (redacted).sh ├── 9.2_bam-readcount.sh └── 9.3_Compare_VAFs.R ├── Auxiliary_files ├── 210215_FunctionsGeneral.R ├── Figure_S5_pipelines.png └── MAESTER_colors.xlsx ├── LICENSE ├── Pre-processing ├── Assemble_fastq.R ├── GoT_QC.R └── Tag_CB_UMI.sh └── README.md /.gitignore: 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