Gen-Assoc

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

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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

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Family-based design

Installation

There is two ways to use M-TDT:

• Command-line : Here is the link to the CLI https://github.com/avalanche-org/m-TDT
• The Graphical User Interface, which will be detailed

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 :

• R
• git
• NodeJs

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

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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 🚀