Name Mode Size
.github 040000
R 040000
data 040000
inst 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
CODE_OF_CONDUCT.md 100644 1 kb
DESCRIPTION 100644 2 kb
LICENSE.md 100644 34 kb
NAMESPACE 100644 1 kb
NEWS.md 100644 3 kb
README.Rmd 100644 4 kb
README.md 100644 5 kb
codecov.yml 100644 0 kb
README.md
# POMA <img src='man/figures/logo.png' align="right" height="139" /> <!-- badges: start --> [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) [![CodeFactor](https://www.codefactor.io/repository/github/pcastellanoescuder/POMA/badge)](https://www.codefactor.io/repository/github/pcastellanoescuder/POMA) [![Last Commit](https://img.shields.io/github/last-commit/pcastellanoescuder/POMA.svg)](https://github.com/pcastellanoescuder/POMA/commits/master) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) <!-- [![R-CMD-check](https://github.com/pcastellanoescuder/POMA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pcastellanoescuder/POMA/actions/workflows/R-CMD-check.yaml) --> <!-- [![Codecov test coverage](https://codecov.io/gh/pcastellanoescuder/POMA/branch/master/graph/badge.svg)](https://codecov.io/gh/pcastellanoescuder/POMA?branch=master) --> | *BioC* branch | Status | Version | Rank | |-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------| | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.14.0-blue.svg)](https://www.bioconductor.org/packages/POMA) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) | | [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.15.17-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) | <!-- badges: end --> The `POMA` package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, `POMA` leverages the standardized `SummarizedExperiment` class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making `POMA` an essential asset for researchers handling omics datasets. <!-- ## push to Bioc (upstream remote at git@git.bioconductor.org) git push upstream main:devel &#10;## push to GitHub (origin remote) git push origin main --> ## Installation To install the Bioconductor last release version: ``` r # install.packages("BiocManager") BiocManager::install("POMA") ``` To install the GitHub version: ``` r # install.packages("devtools") devtools::install_github("pcastellanoescuder/POMA") ``` To install the GitHub devel version: ``` r devtools::install_github("pcastellanoescuder/POMA", ref = "devel") ``` ## Citation Castellano-Escuder 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. ``` bibtex @article{castellano2021pomashiny, title={POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis}, author={Castellano-Escuder, Pol and Gonz{\'a}lez-Dom{\'\i}nguez, Ra{\'u}l and Carmona-Pontaque, Francesc and Andr{\'e}s-Lacueva, Cristina and S{\'a}nchez-Pla, Alex}, journal={PLOS Computational Biology}, volume={17}, number={7}, pages={e1009148}, year={2021}, publisher={Public Library of Science San Francisco, CA USA} } ``` ## News Click [here](https://github.com/pcastellanoescuder/POMA/blob/master/NEWS.md) for the latest package updates.