A benchmark for RNA-seq deconvolution analysis under dynamic testing environments

Table 1 Cellular components and datasets involved in three testing frameworks and variance analysis

Analysis	Cell types	Datasets
Variance analysis	CD8 T cells Whole blood Simulated mixtures (T, B, and mono)	GSE113590 GSE60424 GSE51984
Sim1_simModel	Simulated mixtures (T, B, and mono)	GSE60424 GSE51984 GSE64655
Sim1_libSize	Simulated mixtures (T, B, and mono)	GSE60424 GSE51984 GSE64655
Sim2	6 gradients of cell types: Comp 5–10	GSE60424 GSE51984 GSE64655 GSE115736
Sim3	6 gradients of cell types: Comp 5–10 and one unknown component HCT116	GSE60424 GSE51984 GSE64655 GSE115736 GSE118490

Six gradients of cell types:
Comp 5—T, B, monocytes, neutrophils, and NK cells
Comp 6—T, B, monocytes, neutrophils, NK cells, and eosinophils
Comp 7—T, B, monocytes, neutrophils, NK cells, eosinophils, and myeloid DC
Comp 8—T, B, monocytes, neutrophils, NK cells, eosinophils, myeloid DC, and CD34+ HSC
Comp 9—CD4 T, CD8 T, B, monocytes, neutrophils, NK cells, eosinophils, myeloid DC, and CD34+ HSC
Comp 10—CD4 T, CD8 T, naive B, memory B, monocytes, neutrophils, NK cells, eosinophils, myeloid DC, and CD34+ HSC

ISSN: 1474-760X