PRISM - Poisson RNA-profile Identification in Scaled Mixtures
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2019-11-15, 2019-11-15
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software
software
software
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Description
PRISM is statistical framework that allows simultaneous extraction of a tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples, by exploiting single-cell reference data. This facilitates a separate analysis of cancer cell and the microenvironment phenotypes and of the tumor composition.
Major features:
Estimates both the sample composition (i.e. fraction of the constituent cell types) and expression profiles (i.e. RNA-seq profiles that you would get if you removed the other cell types) at individual bulk sample level
The single-cell reference are treated as data and are subject to the statistical model, which allows the bulk specific profiles to adapt to unmatched patients
An arbitrary number of composing cell types are supported, and the level of the decomposition can be specified by the user or the cell types can be automatically discovered through clustering
The model accounts for the discrete nature of RNA-seq data and models both expression and technical noise or the lack of thereof, with different genes and cell types having varying degrees of variation
For the details about the method and validation, please refer to our publication on the matter.