This project is complex as it is basically three plus experiments in one.
The client had
-2 different cell lines (YUMM5.2 and B16-F10)
-2 different cell line variants (cas 9 control and ITGB2 KO)
-3 different strains (C57BL6_WT, C57BL6_ICAM1_KO, and NGS_T_cell_null)
For a total of 12 different experimental groups. There are several different QC and DE analysis files as I subset the data to make smaller and smaller comparisons at the client's request. For DE it goes bulk_rna-seq_DE_Schatton -> bulk_rna-seq_DE_Schattonv2 -> bulk_rna-seq_DE_Schatton_submodels -> bulk_rna-seq_DE_Schatton_submodels_genes_of_interest.
New Single Cell Data analysis from 2025 (to address reviewer comments) found in the folder Single_cell_public_data TOC for that data also in the same folder.