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

Journal article

Anene, C.A., Taggart, E., Harwood, C., Pennington, D.J. and Wang, J. (2022). Decosus: An R Framework for Universal Integration of Cell Proportion Estimation Methods. Frontiers in genetics. 13, p. 802838. https://doi.org/10.3389/fgene.2022.802838
AuthorsAnene, C.A., Taggart, E., Harwood, C., Pennington, D.J. and Wang, J.
AbstractThe assessment of the cellular heterogeneity and abundance in bulk tissue samples is essential for characterising cellular and organismal states. Computational approaches to estimate cellular abundance from bulk RNA-Seq datasets have variable performances, often requiring benchmarking matrices to select the best performing methods for individual studies. However, such benchmarking investigations are difficult to perform and assess in typical applications because of the absence of gold standard/ground-truth cellular measurements. Here we describe Decosus, an R package that integrates seven methods and signatures for deconvoluting cell types from gene expression profiles (GEP). Benchmark analysis on a range of datasets with ground-truth measurements revealed that our integrated estimates consistently exhibited stable performances across datasets than individual methods and signatures. We further applied Decosus to characterise the immune compartment of skin samples in different settings, confirming the well-established Th1 and Th2 polarisation in psoriasis and atopic dermatitis, respectively. Secondly, we revealed immune system-related UV-induced changes in sun-exposed skin. Furthermore, a significant motivation in the design of Decosus is flexibility and the ability for the user to include new gene signatures, algorithms, and integration methods at run time.
KeywordsGene Expression; R Package; Cell Deconvolution; Method Integration; Immuno-biology
Year2022
JournalFrontiers in genetics
Journal citation13, p. 802838
PublisherFrontiers Media
ISSN1664-8021
Digital Object Identifier (DOI)https://doi.org/10.3389/fgene.2022.802838
Web address (URL)https://www.frontiersin.org/articles/10.3389/fgene.2022.802838/full
Funder/ClientAcademy of Medical Sciences
Publication dates
Online01 Apr 2022
Print01 Jan 2022
Publication process dates
Deposited16 Jun 2022
Accepted author manuscript
License
File Access Level
Open
LicenseCC BY
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Anene, C.A., Taggart, E., Harwood, C.A., Pennington, D.J. and Wang, J., 2022.pdf
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