Welcome to the public repository for the Odisce team, providing a comprehensive suite of packages for (metabol)omics data processing and analysis.
Detailed tutorials about this workflow can be found e.g. in the vignettes of the phenomis, ropls, and biosigner packages.
Feel free to contact us for any question.
| Package | Description | Reference |
|---|---|---|
| Preprocessing | ||
| ionshed | Segmenting LC-MS raw data | Dechaumet et al. |
| MassGAT | Untargeted detection and annotation of LC-HRMS data | Pinart et al. (2026). bioRxiv |
| proFIA | Preprocessing of FIA-HRMS data | Delabrière et al. (2017). Bioinformatics |
| ptairMS | Pre-processing PTR-TOF-MS Data | Roquencourt et al. (2022). Bioinformatics |
| Spec2Xtract | Pre-processing of MS/MS raw spectra | Dechaumet et al. |
| DIANMF | Pre-processing of SWATH DIA data | Karaki et al. (2024). EUSIPCO |
| Post-processing | ||
| phenomis | Post-processing and univariate analysis of MS data | Imbert et al. (2021). Sci. Data. |
| Machine learning | ||
| ropls | PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data | Thévenot et al. (2015). J. Proteome Res. |
| biosigner | Signature discovery from omics data | Rinaudo et al. (2016). Front. Mol. Biosci. |
| ProMetIS | Multi-omics phenotyping of the LAT and MX2 knockout mice | Imbert et al. (2021). Sci. Data. |
| Cheminformatics | ||
| Spec2Annot | Annotation of MS/MS spectra | Dechaumet et al. |
| mineMS2 | Annotation of spectral libraries with exact fragmentation patterns | Delabrière, Gianfrotta et al. (2025). J. Cheminform. |
| biodb | A library and a development framework for connecting to chemical and biological databases | Roger et al. |