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POMA introduces a reproducible and easy-to-use toolkit for visualization, pre-processing, exploration, and statistical analysis of omics datasets. The main aim of POMA is to enable a flexible data cleaning and statistical analysis processes in one comprehensible and user-friendly R package. This package uses the standardized SummarizedExperiment class to achieve the maximum flexibility and reproducibility with other Bioconductor packages.
POMA provides two different Shiny apps both for exploratory data analysis and statistical analysis that implement all POMA functions in two user-friendly web interfaces.
- POMAShiny: Shiny version of this package. https://github.com/pcastellanoescuder/POMAShiny
- POMAcounts: Shiny version for exploratory and statistical analysis of mass spectrometry spectral counts data and RNAseq data. https://github.com/pcastellanoescuder/POMAcounts
The GitHub page is for active development, issue tracking and forking/pulling purposes. To get an overview of the package, see the POMA Workflow vignette.
To install Bioconductor version:
# install.packages("BiocManager")
BiocManager::install("POMA")If you need the GitHub version (not recommended), use:
# install.packages("devtools")
devtools::install_github("pcastellanoescuder/POMA")Castellano-Escuder P, González-Domínguez R, Carmona-Pontaque F, et al. POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis. PLoS Comput Biol. 2021 Jul 1;17(7):e1009148. doi: 10.1371/journal.pcbi.1009148. PMID: 34197462; PMCID: PMC8279420.
Bellio C, Emperador M, Castellano P, et al. GDF15 Is an Eribulin Response Biomarker also Required for Survival of DTP Breast Cancer Cells. Cancers (Basel). 2022 May 23;14(10):2562. doi: 10.3390/cancers14102562. PMID: 35626166; PMCID: PMC9139899.
González-Domínguez R, Castellano-Escuder P, Lefèvre-Arbogast S, et al. Apolipoprotein E and sex modulate fatty acid metabolism in a prospective observational study of cognitive decline. Alzheimers Res Ther. 2022 Jan 3;14(1):1. doi: 10.1186/s13195-021-00948-8. PMID: 34980257; PMCID: PMC8725342.
González-Domínguez R, Castellano-Escuder P, Carmona F, et al. Food and Microbiota Metabolites Associate with Cognitive Decline in Older Subjects: A 12-Year Prospective Study. Mol Nutr Food Res. 2021 Dec;65(23):e2100606. doi: 10.1002/mnfr.202100606. Epub 2021 Oct 28. PMID: 34661340.
Peron G, Gargari G, Meroño T, et al. Crosstalk among intestinal barrier, gut microbiota and serum metabolome after a polyphenol-rich diet in older subjects with “leaky gut”: The MaPLE trial. Clin Nutr. 2021 Oct;40(10):5288-5297. doi: 10.1016/j.clnu.2021.08.027. Epub 2021 Sep 9. PMID: 34534897.
Click here for the latest package updates.
Please note that the ‘POMA’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.