# POMA <img src='man/figures/logo.png' align="right" height="139" />
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| *BioC* branch | Status | Version | Dependencies | Rank |
|-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
| [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [](https://www.bioconductor.org/packages/POMA) | [](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) |
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[**POMA**](http://pcastellanoescuder.github.io/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**](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)
class to achieve the maximum flexibility and reproducibility with other
[Bioconductor](https://bioconductor.org) 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](https://github.com/pcastellanoescuder/POMA) is for
active development, issue tracking and forking/pulling purposes. To get
an overview of the package, see the [*POMA
Workflow*](https://pcastellanoescuder.github.io/POMA/articles/POMA-demo.html)
vignette.
## Installation
To install Bioconductor version:
``` r
# install.packages("BiocManager")
BiocManager::install("POMA")
```
If you need the GitHub version (not recommended), use:
``` r
# install.packages("devtools")
devtools::install_github("pcastellanoescuder/POMA") # or
devtools::install_github("pcastellanoescuder/POMA", ref = "devel")
```
## Citation
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.
### Cited In
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.
## News
Click
[here](https://github.com/pcastellanoescuder/POMA/blob/master/NEWS.md)
for the latest package updates.
## Code of Conduct
Please note that the ‘POMA’ project is released with a [Contributor Code
of
Conduct](https://pcastellanoescuder.github.io/POMA/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.
