/Gen-Assoc

Gen-Assoc is a webservice version of the M-TDT (the multi-locus transmission disequilibrium test) tool. A tool developed to detect family-based multi-locus multi-allelic effects for qualitative or quantitative traits, extended from the original transmission disequilibrium test (TDT).

Primary LanguageJavaScript

mtdtlogoh3abionet

Gen-Assoc

h3abionet

Tools and Web Service work Package
M-TDT tool Documentation.

Multi-Transmission Disequilibrium Test

What is it?

M-TDT (Multi-locus Transmission Disequilibrium Test) is an open source program computing a family-based statistic testing for association between a phenotype and a set of multi-allelic markers. The program is for family-based genome-wide screening of single and joint effects of genetic mutations on infectious disease traits, either qualitative or quantitative traits, regardless of phenotype distribution.

Context

  • Many studies in Africa with recruitment in families (trio, nuclear families data)
  • Study of Infectious disease (multifactorial diseases, complex traits)
  • Need statistical analysis methods and tools to handle data from such studies

Strengths

  • Ability to find joint effects of several markers impacting phenotypes in a context of small sample size
  • Retrieve markers that would be missed by classical approaches
  • Handles of main statistical issues like:
    • non-specified distribution of traits
    • related individuals
    • population admixture
    • linkage disequilibrium among markers

Family-based design

Family-based design

Installation

There is two ways to use M-TDT:

GUI : Web Application

You can use the tool currently deployed on the Institut Pasteur servers: (link)

If you want to install the GUI version locally you have two ways to do so:

1. Node Package Manager (npm)

You need to install :

1 - Clone repository

$  git clone https://github.com/avalanche-org/Gen_Assoc.git

2 - Move to Gen_Assoc/apps folder and install the required dependencies

$ cd Gen_Assoc; cd apps
$ npm install

3 - Run the application

$ npm run build

Open your browser and type http://localhost:4000/

Here your are !

To stop the application, type Ctrl+c in terminal. If the application crashes, type Ctrl+c and rerun npm run build

2. Docker

For this section Docker (Docker) is required.

The Webservice Application docker image is available on docker registry

Docker

Open your terminal:

docker pull jukoo/m-tdt:stablev1

To launch the docker application

$  docker run -d -p <localport>:<containerPort> jukoo/m-tdt:stablev1

The default port of the container is 4000

example:

docker run -d -p 3000:4000 jukoo/m-tdt:stablev1

💡 If you get a warning indicating a platform mismatch between the requested platform for the Docker image and the platform detected on the host machine, then add `--platform linux/amd64` to the command

Open your browser and type http://localhost:3000/

Here you are 🚀