Rare Disease Workflows
This repo contains a list of workflows designed for accerating the interpretation of rare-disease data, currently applied to data within the NF-OSI.
The goal of this repository is to faciliate harmonization across rare-disease datasets that are deposited onto Synapse. These workflows will be centered around various stages of analysis, shown below.
Data Harmonization workflows
We have built a number of workflows that re-process raw data uploaded to Synapse to create a single data repository. All harmonized datasets will be colated in a single table that should be uploaded every time we have a new dataset processed.
| Data Type | Description | Location | Destinations | Status |
|---|---|---|---|---|
| RNA-Seq | This workflow runs Salmon alignment from FASTQ files to populate a both a public and private Synapse table that stores all NF-related gene expression data. | rna-seq-workflow/ | JHU Biobank RNA-Seq | Complete |
| Exome/WGS-Seq | This workflow currently runs vcf2maf on uploaded vcf files and stores them on Synapse. |
gene-variant-workflow | JHU Biobank Exome Seq | Currently processed files, needs to be updated to store data on synapse. Currently being uploaded to run DeepVariant caller |
| Somatic variant caller | This workflow should take the raw data and call somatic variants. | somatic-variant-caller/ | TBD | Currently adding Synapse pieces to Kids-First variant caller |
| Drug-Sensitivity Data | This workflow takes drug-sensitivity data and combines it to a single file. | drug-screening-workflow | Table TBD | Still requires table update |
As more data types are added we will continue to add more workflows.
Research projects/workflows
Building upon these standardized datasets are workflows that take the data generated by the data harmonization steps above to identify new scientific hypotheses.
| Project name | Description | Data Type | Results Tables | Status |
|---|---|---|---|---|
| DTEN | Drug-target expression network takes gene expression data and identifies relevant drug targets. | RNA-Seq | DTEN Nodes, [DTEN Terms]() | Currently required update to do analysis of network results. |
| CDOM | Combinatorial domain mutation analysis | Exome/WGS-Seq | TBD | Under development |
| [Latent variable analysis]() | We are comparing various latent variable approaches to characterize gene expression data | RNA-Seq | Under development | |
| [Gene mutation feature selection]() | This project evaluates the ability of specific genes to predict tumoe type | Under development | ||
| [Drug sensitivity analysis]() | This project looks to identify difference in drug sensitivy across cell lines representing different tumor types | Under development |
Results extraction workflows
This is a placeholder for tool we develop to transfer the data into a more visualizable format, such as shiny apps or ETL tools.