Gene expression profiles and analytics. Developed by UNM for the NIH Data Commons Pilot Phase Consortium as part of Key Capability 8, Scientific Use Cases. GTEx RNAseq pre-processing and analysis workflows initially developed by Oleg Ursu and Giovanni Bocci. Jupyter notebooks and Python/Pandas port by Jeremy Yang. Dockerization and Cloud/AWS tooling by Mike Garcia. See R Shiny app at https://unmtid-shinyapps.net/exfiles/.
- Python 3.6+; Pandas, BioClients
- R 3.6+; readr, data.table, labdsv, wCorr
See WORKFLOW.md
| Term | Description |
|---|---|
| TPM | Transcripts per million |
| Log2FoldChange | LOG2(TPM_F/TPM_M) |
| Tau | Tissue specificity index (Yanai et al., 2004) |
- GTEx Documentation
- GTEx Datasets (with data dictionaries).