This repository contains the computational workflows, metadata, and supporting resources for all PrecisionTox multi-omics data descriptors.
The content is intended to ensure transparency, reproducibility, and reuse of the associated multi-omics datasets.
Data descriptors themselves are published separately (e.g., in journals such as Scientific Data), with raw data deposited in domain-specific repositories.
Datasets involve multi-omics profiling:
- Transcriptomics (RNA-seq)
- Metabolomics and lipidomics (UHPLC–MS)
Each dataset is generated under a harmonised experimental design to support cross-species comparison.
Together, these datasets provide a time- and dose-resolved multi-omics resource for studying the biological impacts of chemical exposures.
The table below summarises the PrecisionTox data descriptors, with links to the corresponding datasets, analysis workflows, and supporting resources.
| Common Name | Scientific Name | Data Descriptor | Transcriptomics (RNA-seq) | Metabolomics & lipidomics | Workflows |
|---|---|---|---|---|---|
| Water flea | Daphnia magna | [Link to publication] | E-MTAB-17460 | [MetaboLights ID] | daphnia_magna/ |
| Fruit fly | Drosophila melanogaster | [TBD] | [TBD] | [TBD] | drosophila_melanogaster/ |
| Zebrafish | Danio rerio | [TBD] | [TBD] | [TBD] | danio_rerio/ |
| Nematode (roundworm) | Caenorhabditis elegans | [TBD] | [TBD] | [TBD] | caenorhabditis_elegans/ |
| African clawed frog | Xenopus laevis | [TBD] | [TBD] | [TBD] | xenopus_laevis/ |
ptox-data-descriptors/
│
├── drosophila_melanogaster/
├── daphnia_magna/
├── caenorhabditis_elegans/
├── danio_rerio_embryo/
├── xenopus_laevis_embryo/
├── hepg2_cells/
│
└── docs/
└── images/
└── banner.jpg
daphnia_magna/
├─ metabolomics/
│ ├─ MTBLS1234/
│ │ ├─ configs/
│ │ │ ├─ config_schema.json
│ │ │ ├─ Dmagna_HILIC_POS_config.json
│ │ │ └─ Dmagna_LIPIDS_POS_config.json
│ │ ├─ modules/
│ │ │ ├─ figures_pca.R
│ │ │ ├─ figures_rsd.R
│ │ │ ├─ general_util.R
│ │ │ ├─ pmp_util.R
│ │ │ └─ xeno_util.R
│ │ ├─ resources/
│ │ │ ├─ master_list_HILIC_POS.csv
│ │ │ ├─ master_list_LIPIDS_POS.csv
│ │ │ ├─ metadata.xlsx
│ │ │ └─ notebook-theme.css
│ │ ├─ environment_peak_matrix_processing.yml
│ │ ├─ environment_preprocessing.yml
│ │ ├─ exploratory_statistics.Rmd
│ │ ├─ peak_matrix_processing.Rmd
│ │ ├─ preprocessing.Rmd
│ │ ├─ run_workflow.R
│ │ └─ README.md
├─ transcriptomics/
│ ├─ E-MTAB-5678/
│ │ ├─ mapping_performance.Rmd
│ │ ├─ deseq2_preprocessing.Rmd
│ │ ├─ ptox_pilot_daphnia.RData
│ │ ├─ scripts/
│ │ │ ├─ nextflow_trim.sh
│ │ │ ├─ nxf_trim.nf
│ │ │ ├─ nextflow_star_transcriptome.sh
│ │ │ ├─ nxf_star_transcriptome.nf
│ │ │ ├─ qualimap_for_star_bam_sortedByCoord.sh
│ │ │ ├─ samtools_sortedByName.sh
│ │ │ └─ htseq_quantification.sh
│ │ ├─ resources/
│ │ │ └─ metadata.xlsx
│ │ └─ README.md
This repository is designed to support fully reproducible data processing and analyses:
- Version-controlled workflows and scripts
- Documented workflow steps
- Use of established tools (e.g., R / Bioconductor ecosystems)
Where implemented, continuous integration (CI) supports:
- Validation of code execution
- Workflow consistency checks
- Dependency management
Releases of this repository are archived on Zenodo, providing:
- Persistent DOIs for citation
- Long-term preservation of code and workflows
Zenodo records will be linked here as releases become available.
This work is part of the PrecisionTox project, funded by the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 965406).
- PrecisionTox website: https://precisiontox.org/
- Repository: https://github.com/precisiontox/ptox-data-descriptors
- Zenodo: [to be added]
For questions or collaboration inquiries, please contact the repository maintainers or authors of the associated data descriptors.