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. 2016 Dec 15;32(24):3842-3843.
doi: 10.1093/bioinformatics/btw535. Epub 2016 Aug 16.

ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data

Amit Frishberg  1 , Avital Brodt  1 , Yael Steuerman  1 , Irit Gat-Viks  1
Affiliations

ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data

Amit Frishberg et al. Bioinformatics. .

Abstract

: The composition of immune-cell subsets is key to the understanding of major diseases and pathologies. Computational deconvolution methods enable researchers to investigate immune cell quantities in complex tissues based on transcriptome data. Here we present ImmQuant, a software tool allowing immunologists to upload transcription profiles of multiple tissue samples, apply deconvolution methodology to predict differences in cell-type quantities between the samples, and then inspect the inferred cell-type alterations using convenient visualization tools. ImmQuant builds on the DCQ deconvolution algorithm and allows a user-friendly utilization of this method by non-bioinformatician researchers. Specifically, it enables investigation of hundreds of immune cell subsets in mouse tissues, as well as a few dozen cell types in human samples.

Availability and implementation: ImmQuant is available for download at http://csgi.tau.ac.il/ImmQuant/ CONTACT: iritgv@post.tau.ac.ilSupplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
The ImmQuant pipeline
See this image and copyright information in PMC

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