Application of software enabling computational deconvolution of bulk RNA-sequencing data to immune cell profiles of patient samples

This is the accepted iPC deliverable D7.1 „Application of software enabling computational deconvolution of bulk RNA-sequencing data to immune cell profiles of patient samples“. Computational deconvolution of bulk RNA-sequencing data to infer cell type composition of a sample is challenging. Benchmarking of various computational deconvolution tools revealed various data processing parameters that impact deconvolution accuracy and revealed the importance of a complete reference matrix. As a complete reference matrix is often not available, an algorithm was designed that can handle missing cell types. This algorithm can be applied to establish the immune cell repertoire of primary tumor biopsies without prior knowledge of the full spectrum of cell types in the biopsy