ArticleBioinformatics advances2024
DECOMICS, a shiny application for unsupervised cell type deconvolution and biological interpretation of bulk omic data.
Article in Bioinformatics advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- IECP: iterative equilibration of cell-type expression profiles improves accuracy of reference-free deconvolution.Bioinformatics (Oxford, England) · 2026Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: Unsupervised deconvolution algorithms are often used to estimate cell composition from bulk tissue samples. However, applying cell-type deconvolution and interpreting the results remain a challenge, even more without prior training in bioinformatics. Here, we propose a tool for estimating and identifying cell type composition from bulk transcriptomes or methylomes. DECOMICS is a shiny-web application dedicated to unsupervised deconvolution approaches of bulk omic data. It provides (i) a variety of existing algorithms to perform deconvolution on the gene expression or methylation-level matrix, (ii) an enrichment analysis module to aid biological interpretation of the deconvolved components, based on enrichment analysis, and (iii) some visualization tools. Input data can be downloaded in csv format and preprocessed in the web application (normalization, transformation, and feature selection). The results of the deconvolution, enrichment, and visualization processes can be downloaded. Availability and implementation: DECOMICS is an R-shiny web application that can be launched (i) directly from a local R session using the R package available here: https://gitlab.in2p3.fr/Magali.Richard/decomics (either by installing it locally or via a virtual machine and a Docker image that we provide); or (ii) in the Biosphere-IFB Clouds Federation for Life Science, a multi-cloud environment scalable for high-performance computing: https://biosphere.france-bioinformatique.fr/catalogue/appliance/193/.
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Registered trials
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