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POMA

:package: Omics Data Analysis Tools

https://github.com/pcastellanoescuder/poma

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
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  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.0%) to scientific vocabulary

Keywords

bioconductor bioinformatics data-visualization dimension-reduction exploratory-data-analysis machine-learning omics-data-integration pipeline pre-processing r r-package rstats statistical-analysis user-friendly workflow

Keywords from Contributors

ontology
Last synced: 6 months ago · JSON representation

Repository

:package: Omics Data Analysis Tools

Basic Info
  • Host: GitHub
  • Owner: pcastellanoescuder
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 40.7 MB
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 5
  • Open Issues: 0
  • Releases: 2
Topics
bioconductor bioinformatics data-visualization dimension-reduction exploratory-data-analysis machine-learning omics-data-integration pipeline pre-processing r r-package rstats statistical-analysis user-friendly workflow
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License Code of conduct

README.Rmd 

---
output: github_document
---

# POMA 

  
  
  [![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)
  
  

| _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-1.16.0-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-1.17.6-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) 	|

  

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.   



## Installation

To install the Bioconductor last release version:

```{r, eval = FALSE}
# install.packages("BiocManager")
BiocManager::install("POMA")
```

To install the GitHub version:

```{r, eval = FALSE}
# install.packages("devtools")
devtools::install_github("pcastellanoescuder/POMA")
```

To install the GitHub devel version:

```{r, eval = FALSE}
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.

Owner

  • Name: Pol Castellano Escuder
  • Login: pcastellanoescuder
  • Kind: user
  • Location: Durham, NC, US
  • Company: Duke Molecular Physiology Institute

Bioinformatician at Duke University. Computational Biology & Data Science | Multi-omics, Machine Learning, AI & Software Development

GitHub Events

Total
  • Push event: 5
Last Year
  • Push event: 5

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 271
  • Total Committers: 3
  • Avg Commits per committer: 90.333
  • Development Distribution Score (DDS): 0.369
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Pol Castellano Escuder p****s@g****m 171
pcastellanoescuder p****l@M****l 92
Nitesh Turaga n****a@g****m 8

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 6
  • Average time to close issues: 8 days
  • Average time to close pull requests: 14 days
  • Total issue authors: 7
  • Total pull request authors: 1
  • Average comments per issue: 2.13
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adamsorbie (2)
  • pbaCamille (1)
  • rfilipesoares (1)
  • pcastellanoescuder (1)
  • Arm3de (1)
  • linlennypinawa (1)
  • MPietzke (1)
Pull Request Authors
  • pcastellanoescuder (6)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 11,560 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: POMA

Tools for Omics Data Analysis

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 11,560 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 25.7%
Downloads: 77.2%
Maintainers (1)
polcaes@gmail.com
Last synced: 6 months ago