Data-driven Hypothesis

Data-driven hypothesis is a resource for identifying novel functions for human genes developed by the Hirschey Lab. A typical use case starts by querying a gene, identifying genes that share similar patterns or behaviors across various measures, in order to discover new novel genes in established processes or new processes for well-studied genes.

Querying Data

Visit www.datadrivenhypothesis.org to query genes, generate data, and download reports.

Methods

Visit www.datadrivenhypothesis.org to view detailed methods for this project. Alternatively, after generating data files, knit code/methods.Rmd for the complete methods summary.

Generating/Recreating Data

The .R scripts in the /code directory are used to generate files in the /data directory. If you have R, the required libraries installed you can generate the data by running:

mkdir data
Rscript code/generate_data.R

If you have an NCBI API key this can speed up portions of the data generation process. Before running Rscript code/generate_data.R export your NCBI API key to an environment variable named ENTREZ_KEY like so:

export ENTREZ_KEY="your-key-here"

Singularity and Slurm

On systems that support the singularity container runtime, we recommend using our container image to run the data-generating R scripts with the required dependencies.

Generating data under singularity is also demonstrated in the submit-slurm-jobs.sh. It requires a config.sh script. This config script has three optional environment variables: ENTREZ_KEY, DDH_EMAIL, DDH_UPLOAD_RESULTS. An example config.sh script that will email you about job progress and upload the results looks like so:

export ENTREZ_KEY="your-key-here"
export DDH_EMAIL="your-email@email.com"
export DDH_UPLOAD_RESULTS="TRUE"

This DDH_UPLOAD_RESULTS requires you to create a .ddsclient configuration file in your home directory on the cluster. See instructions to setup a DukeDS config file. to set the ENTREZ_KEY environment variable. You can also speicfy a DDH_EMAIL email address to be emailed with job progress.

This script can be run like so from a slurm cluster:

./submit-slurm-jobs.sh

This script will submit multiple jobs that will run one after another with differing requirements. When this script finishes it will upload the results to DukeDS service.