www.snpstats.net)

SNPStats is a simple, ready-to-use software which has been designed to analyze genetic-epidemiology studies of association using SNPs.

You can upload your data and, for each selected SNP, you will receive:

Allele and genotype frequencies
Test for Hardy-Weinberg equilibrium
Analysis of association with a response variable based on linear or logistic regression
Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive
Analysis of interactions (gene-gene or gene-environment)

If multiple SNPs are selected:

Linkage disequilibrium statistics
Haplotype frequency estimation
Analysis of association of haplotypes with the response
Analysis of interactions (haplotypes-covariate)

SNPstats was developed by Xavier Solé at the Unit of Biomarkers and Susceptibility of the Cancer Prevention and Control Program, Catalan Institute of Oncology (https://www.icoprevencio.cat)

Please cite the paper:

SNPStats: a web tool for the analysis of association studies Xavier Sole, Elisabet Guino, Joan Valls, Raquel Iniesta, and Victor Moreno Bioinformatics 2006 22: 1928-1929.

Dockerfile based on alpine-r & alpine-apache-php

Alpine-r @artemklevtsov

Alpine-apache-php @wichon

SNPstats is based on R. View R-project license information for the software contained in this image. The main R libraries used are genetics and haplo.stats

Install on your computer:

git clone https://github.com/victor-moreno/snpstats-docker
cd snpstats-docker

Build

From the folder where Dockerfile is located:

docker build --no-cache -t snpstats .

Usage

docker run -d -p 8083:80 --name snpstats snpstats

open http://localhost:8083

Notes

Yo can change the browser port (8083) to any of your choice.

The application keeps temporary files. To avoid that the image grows, you can expose temporary folders and clean them periodically:

dir=`pwd`
mkdir $dir/tmp_html
mkdir $dir/tmp_scripts

docker run -d -p 8083:80 --name snpstats -v $dir/tmp_scripts:/app/snpstats/tmp_scripts -v $dir/tmp_html:/app/snpstats/tmp_html snpstats

To improve and debug, extract the code and expose it:

tar xzf snpstats.tar.gz
docker run -d -p 8083:80 --name snpstats -v $"`pwd`"/snpstats:/app/snpstats snpstats

The you can easily modifiy the code inside the container.

Problems & Bugs

The code was written in 2006 and has been minimmaly updated to support newer versions of R, but still uses an old version of haplo.stats package to reduce the dependence load. It also will work without modifications with current versions.

Some problems with data or serioulsy problematic models with undefined solutions may crash the R code.

Please report any problem or comments and we'll try to address it.