pgxcentre/exphewas

Browser for the results of a gene-PC based pheWAS in the UK Biobank

This repository contains the code behind ExPheWas. A thorough description of the project can be found either in the project's documentation or in the manuscript.

Overview of the repository

Briefly, the exphewas directory contains the python package that powers the web application's backend (API, web application and database). The exphewas python package can be installed (e.g. using pip install .. Once this is done, a command-line utility will be available that offers various housekeeping utilities like data loading or database initialization.

The code for the frontend is in the frontend directory. The command npm run build can be used from that directory to build the javascript from the frontend. The code for all D3.js graphs can be found there.

Configuration

Configuration only requires a database string for SQLAlchemy and the path where the frontend gets built.

export EXPHEWAS_DATABASE_URL=postgresql+psycopg2://user:password@host/dbname
export EXPHEWAS_STATIC_FOLDER=.../exphewas/frontend/dist

Issue tracker

The issue tracker is a good way to send us suggestions or to report problems with any aspect of ExPheWas.

Citation

Marc-André Legault, Louis-Philippe Lemieux Perreault, and Marie-Pierre Dubé. "ExPheWas: a browser for gene-based pheWAS associations." medRxiv (2021).

exphewas's Issues

Add documentation for API /cisMR

gene2vec improvements

• Set default variance explained at 95%
• Expose MAF threshold as parameter
• Allow sex-stratified PCA
• Select only bi-allelic SNPs
• Save CSV as gzip compressed by default
• Allow imputation quality filtering (?)

Instrumental variable (eQTL and pQTL) -> mRNA-expression, protein level -> outcome (disease/phecode)

Dear Team,

I am wondering is there any timeline to implement: Instrumental variable (eQTL and pQTL) -> mRNA-expression, protein level -> outcome (disease/phecode).

Thanks.

Shicheng

Suggest: README with link to pre-print and browser

ExPheWas seems awesome to me!

The GitHub, however, feels less helpful than it could.

I suggest to add a README with links to the pre-print (and accepted manuscript in the future) and browser, such as the text below. That would help me and others to find the other parts.

Sure I can make a Pull Request to the dev branch if asked :-)

Cheers, Richel

ExPheWas

ExPheWas is [what it is] and can be found at https://exphewas.statgen.org.

Citation

Legault, Marc-André, Louis-Philippe Lemieux Perreault, and Marie-Pierre Dubé. "ExPheWas: a browser for gene-based pheWAS associations." medRxiv (2021).

Manuscript can be found here

batch download of all cis MR results

I was wondering if it is possible to download all the cis MR results for all genes, all exposures and all outcomes. Thanks.