quanTIseq – quantifying immune contexture of human tumors

quanTIseq is the first computational pipeline for the quantification of Tumor-infiltrating Immune cells from raw RNA-seq data and images of haematoxylin and eosin (H&E)-stained tissue slides.

quanTIseq can estimate the cell fractions of ten different immune cell types and the proportions of uncharacterized cells from RNA-seq data obtained from heterogeneous samples (e.g. blood samples or tissue specimens).

As data pre-processing can have a strong impact on the final estimates, quanTIseq implements a full analytical pipeline, consisting of:

  • Read pre-processing;
  • Quantification of gene expression;
  • Deconvolution of cell fractions using a novel immune-cell signature matrix;
  • Computation of cell densities using H&E images, when available.

Using extensive validation on simulated data, published data, data from blood cell mixtures, and two independent cancer data sets, researchers from the Medical University of Innsbruck demonstrated that quanTIseq can faithfully and quantitatively infer immune cell fractions from heterogeneous samples profiled with RNA-seq and can be easily applied to large collections of bulk-tumor RNA-seq data to portray the immune contexture of human tumors.


quanTIseq characterizes the immune contexture of human tumors from expression and image data. Cell fractions are estimated from expression data and then scaled to cell densities (cells/mm2) using total cell densities extracted from imaging data.

Availability – quanTIseq tool is available at: http://icbi.i-med.ac.at/software/quantiseq/doc/index.html

Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Posch W, Wilflingseder D, Sopper S, Jsselsteijn M, Johnsons D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Balko J, de Miranda NF, Trajanoski Z. (2018) quanTIseq: quantifying immune contexture of human tumors. bioRXiv [Epub ahead of print]. [abstract]

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