This module enables the collection of mRNA patient data using the cptac Python package to collect mRNA data for one of six available cancer types. This module includes the following:
| File name | Description |
|---|---|
getAllDatasets.py | This script is run within the Docker build process to get all datasets into the Python environment |
mRNADataSetsCLI.py | This script is the primary tool to pull a specific cancer data type |
Dockerfile | This file contains the two scripts above and the cptac Python package |
mrna-data-cwl-tool.cwl | This is a CWL tool to run the Docker image with the command line tool |
There are three ways to get mRNA data, depending on your environment. Each one should output a file.tsv in your local directory
Simply run the command
python mRNADataSetsCLI.py --cancerType=brca
Then you can run the command via the docker interactive mode
docker build . -t mrna-module
docker run --volume $PWD:/tmp -ti mrna-module mRNADataSetsCLI.py --cancerType=brca
Here we have an example using the cwl-tool engine, but this should run any other engine as well.
cwl-tool mrna-data-cwl-tool.cwl --cancerType brca
| Dataset name | Description | Data reuse status | Publication link |
|---|---|---|---|
| Brca | breast cancer | no restrictions | https://pubmed.ncbi.nlm.nih.gov/33212010/ |
| Ccrcc | clear cell renal cell carcinoma (kidney) | no restrictions | https://pubmed.ncbi.nlm.nih.gov/31675502/ |
| Colon | colorectal cancer | no restrictions | https://pubmed.ncbi.nlm.nih.gov/31031003/ |
| Endometrial | endometrial carcinoma (uterine) | no restrictions | https://pubmed.ncbi.nlm.nih.gov/32059776/ |
| **Gbm | glioblastoma | password access only | unpublished** |
| Hnscc | head and neck squamous cell carcinoma | no restrictions | https://pubmed.ncbi.nlm.nih.gov/33417831/ |
| **Lscc | lung squamous cell carcinoma | password access only | unpublished** |
| Luad | lung adenocarcinoma | no restrictions | https://pubmed.ncbi.nlm.nih.gov/32649874/ |
| Ovarian | high grade serous ovarian cancer | no restrictions | https://pubmed.ncbi.nlm.nih.gov/27372738/ |
| **Pdac | pancreatic ductal adenocarcinoma | password access only | unpublished** |
As such, datasets have been updated to following (added hnscc): ['brca', 'ccrcc', 'endometrial', 'colon', 'ovarian', 'hnscc', 'luad']
Content type
Image
Digest
sha256:788fa6f02…
Size
519.5 MB
Last updated
over 2 years ago
docker pull tumordeconv/mrna-data