shugamoe
commented
4 months ago Anything with a "Score" in the name combines multiple cells.
See https://github.com/dviraran/xCell/blob/20e2919eefd37e15af35f29f4944e30697098a28/R/xCell.R#L217
[1] "Adipocytes" "Astrocytes"
[3] "B-cells" "Basophils"
[5] "CD4+ T-cells" "CD4+ Tcm"
[7] "CD4+ Tem" "CD4+ memory T-cells"
[9] "CD4+ naive T-cells" "CD8+ T-cells"
[11] "CD8+ Tcm" "CD8+ Tem"
[13] "CD8+ naive T-cells" "CLP"
[15] "CMP" "Chondrocytes"
[17] "Class-switched memory B-cells" "DC"
[19] "Endothelial cells" "Eosinophils"
[21] "Epithelial cells" "Erythrocytes"
[23] "Fibroblasts" "GMP"
[25] "HSC" "Hepatocytes"
[27] "Keratinocytes" "MEP"
[29] "MPP" "MSC"
[31] "Macrophages" "Macrophages M1"
[33] "Macrophages M2" "Mast cells"
[35] "Megakaryocytes" "Melanocytes"
[37] "Memory B-cells" "Mesangial cells"
[39] "Monocytes" "Myocytes"
[41] "NK cells" "NKT"
[43] "Neurons" "Neutrophils"
[45] "Osteoblast" "Pericytes"
[47] "Plasma cells" "Platelets"
[49] "Preadipocytes" "Sebocytes"
[51] "Skeletal muscle" "Smooth muscle"
[53] "Tgd cells" "Th1 cells"
[55] "Th2 cells" "Tregs"
[57] "aDC" "cDC"
[59] "iDC" "ly Endothelial cells"
[61] "mv Endothelial cells" "naive B-cells"
[63] "pDC" "pro B-cells"
[65] "ImmuneScore" "StromaScore"
[67] "MicroenvironmentScore"
Where do you find what the valid values are to use with the argument
cell.types.usein the functionxCellAnalysis().