Table 2.

Evaluation of deconvolution pipelines with real mixtures.

	Heterogeneous input	Reference matrix	Marker information	Expected proportions
Bulk deconvolution methodologies	9 human bulk PBMCs	Bulk RNA-seq of monocytes, B cells, natural killer, dendritic cells and T cells (SRA accession from Supplementary Table 1)	Markers for monocytes, B cells, natural killer, dendritic cells and T cells obtained from 10x scRNA-seq data	Flow cytometry measurements
Deconvolution methods using scRNA-seq as reference	9 human bulk PBMCs	10× scRNA-seq data excluding CD34+ cells	No prior information	Flow cytometry measurements

Scenarios used to assess the performance of the different deconvolution methods using bulk RNA-seq from nine PBMCs samples.