A Biodepot workflow builder (Bwb) implementation of a metabolomics preprocessing pipeline using the PCPFM (Python-Centric Pipeline For Metabolomics). Original project GitHub can be found at https://github.com/shuzhao-li-lab/MorPhiC_Data_Releases.
(Current state of workflow is implementing generalized processing and analysis of metabolomics data. A structured workflow to be shown in the near future.)
Expected data inputs are metabolomics .raw or .mzML files. Any .raw files must be converted to .mzML, a pre-processing step that is included in this workflow.
- Bwb
- Python >=3.7
- PCPFM >=1.1.3
- Docker
Mitchell, J.M., Chi, Y., Thapa, M., Pang, Z., Xia, J. and Li, S., 2024. Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline. PLOS Computational Biology, 20(6), p.e1011912. (https://doi.org/10.1371/journal.pcbi.1011912)
Li, S., Siddiqa, A., Thapa, M., Chi, Y. and Zheng, S., 2023. Trackable and scalable LC-MS metabolomics data processing using asari. Nature Communications, 14(1), p.4113. (https://www.nature.com/articles/s41467-023-39889-1)
https://github.com/shuzhao-li-lab/PythonCentricPipelineForMetabolomics