software.Rmd

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title: "Software"
---

#### **Visit our GitHub site: [github.com/odisce](https://github.com/odisce)**

## **R packages**

![](images/odisce_software.png)

-   **biodb**: a library and a development framework for connecting to chemical and biological databases ([DOI:10.18129/B9.bioc.biodb](https://doi.org/doi:10.18129/B9.bioc.biodb))

-   **biosigner**: signature discovery from omics data ([DOI:10.18129/B9.bioc.biosigner](https://doi.org/10.18129/B9.bioc.biosigner))

-   **phenomis**: post-processing and univariate analysis of MS data ([DOI:10.18129/B9.bioc.phenomis](https://doi.org/10.18129/B9.bioc.phenomis))

-   **proFIA**: preprocessing of FIA-HRMS data ([DOI:10.18129/B9.bioc.proFIA](https://doi.org/10.18129/B9.bioc.proFIA))

-   **ProMetIS**: multi-omics phenotyping of the LAT and MX2 knockout mice (<https://github.com/IFB-ElixirFr/ProMetIS>)

-   **ptairMS**: Pre-processing PTR-TOF-MS Data ([DOI:10.18129/B9.bioc.ptairMS](https://doi.org/10.18129/B9.bioc.ptairMS))

-   **ropls**: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data ([DOI:10.18129/B9.bioc.ropls](https://doi.org/10.18129/B9.bioc.ropls))

## **Datasets; [MetaboLights](http://www.ebi.ac.uk/metabolights/index) repository**

-   [MTBLS1903](https://www.ebi.ac.uk/metabolights/MTBLS1903): ProMetIS: deep phenotyping of knock-out mice by proteomics and metabolomics.

-   [MTBLS404](https://www.ebi.ac.uk/metabolights/MTBLS404): Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses ('Sacurine' data set).

-   [MTBLS148](https://www.ebi.ac.uk/metabolights/MTBLS148): Impact of collection conditions on the metabolite content of human urine samples as analyzed by liquid chromatography coupled to mass spectrometry and nuclear magnetic resonance spectroscopy.

## **Galaxy modules; [Galaxy](https://toolshed.g2.bx.psu.edu) toolshed**

-   Batch Correction (in collaboration with Jean-Francois Martin, Melanie Petera, Marion Landi and Franck Giacomoni)

-   Biosigner

-   Heatmap

-   Multivariate

-   proFIA

-   Quality Metrics (in collaboration with Melanie Petera)

-   Univariate (in collaboration with Marie Tremblay-Franco)

## **Workflows and histories; [Workflow4Metabolomics](http://workflow4metabolomics.org/referenced_W4M_histories) e-infrastructure**

-   W4M00001_Sacurine-statistics ([DOI:10.15454/1.4811121736910142E12](http://dx.doi.org/10.15454/1.4811121736910142E12))

-   W4M00002_Sacurine-comprehensive ([DOI:10.15454/1.481114233733302E12](http://dx.doi.org/10.15454/1.481114233733302E12))

-   W4M00003_Diaplasma ([DOI:10.15454/1.4811165052113186E12](http://dx.doi.org/10.15454/1.4811165052113186E12))