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Decosus: An R Framework for Universal Integration of Cell Proportion Estimation Methods.

Chinedu A Anene1,2, Emma Taggart3, Catherine A Harwood4,5

  • 1Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.

Frontiers in Genetics
|April 18, 2022
PubMed
Summary

Decosus, an R package, integrates seven cell deconvolution methods for improved accuracy in analyzing bulk tissue gene expression profiles. It offers stable performance across datasets and user flexibility for new signatures and algorithms.

Keywords:
R packagecell deconvolutiongene expressionimmuno-biologymethod integration

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Genomics

Background:

  • Assessing cellular heterogeneity and abundance in bulk tissues is crucial for understanding organismal states.
  • Existing computational methods for estimating cell abundance from bulk RNA-Seq data show variable performance.
  • Benchmarking these methods is challenging due to the lack of ground-truth cellular measurements.

Purpose of the Study:

  • To introduce Decosus, an R package that integrates seven cell deconvolution methods and signatures.
  • To provide a flexible and robust tool for deconvoluting cell types from gene expression profiles.
  • To enable users to incorporate novel gene signatures, algorithms, and integration methods.

Main Methods:

  • Integration of seven distinct cell deconvolution algorithms and gene expression signatures.
  • Development of an R package (Decosus) for streamlined analysis.
  • Benchmarking against datasets with known ground-truth cellular composition.

Main Results:

  • Decosus demonstrated consistently stable and superior performance compared to individual deconvolution methods across various datasets.
  • Application of Decosus to skin samples confirmed known immune cell polarization in psoriasis and atopic dermatitis.
  • UV-induced immune system changes in sun-exposed skin were identified.

Conclusions:

  • Decosus provides a reliable and adaptable platform for cell type deconvolution from gene expression data.
  • The integrated approach enhances the accuracy and stability of cell abundance estimation.
  • The package facilitates novel discoveries in tissue-specific immune responses and disease characterization.