COMETH Training course

COMETH training course : objectives
Digital platforms
Material to download
- For medical group
- For bioinformatic group
Presentation supports
- DAY1
- DAY2
Course format and program
Target Group
Registration
Trainers

COMETH training course : objectives

15-16 Feb.2021, ONLINE

This 2-day online course aims to train clinicians to the use of cutting edge computational methods to quantify tumor heterogeneity through a dedicated user-friendly web interface.

Registration deadline extension: 10 January 2021

Digital platforms

Zoom plenary sessions

For all participants:

Please register to DAY1 zoom session
Please register to DAY2 zoom session

Discord discussion platform

For all participants:

Create an account on discord
Download discord application (highly recommanded to ease the exchanges between participants)
Join the COMETH training forum

Codabench

For computational participants:

Go to the application : Codabench platform for data challenges
create an account on the platform
register to the COMETH deconvolution data challenge
Tutorial on the use of the codabench platform

COMETH web application

For clinician participants:

Go to the application: COMETH user-friendly web application
create an account on the platform
Tutorial on the use of the cometh web application

COMETH Docker image deconExplorer

For those who want to run the deconvolution and interpretation app locally, we provide a docker image allowing to run all steps of the analysis locally, through your web browser. We provide the instructions for uses running a macOS or linux operating system!

download and install the docker Dektop software for your OS
open a terminal and type the following commands:

cd ~
docker pull ashwinikrsharma/mrna_meth_decon:latest
git clone https://github.com/ashwini-kr-sharma/ShinyCompExplore.git
docker run --rm -it -p 3838:3838 -v ~/ShinyCompExplore:/srv/shiny-server/ ashwinikrsharma/mrna_meth_decon

open a web browser, and type localhost:3838 in the address bar

Good to go!

COMETH shiny application

Shiny app comExplorer
Shiny app DdconExplorer (similar to comExplorer, with some deconvolution methods implemented)

Material to download

Practical work will differ according to your affectation (medical or bioinformatic group). Please check your affectation and download the corresponding material here.

For medical group

Datasets

We have prepared toy expression datasets from the TCGA public cancer database (including clinical annotation tables).

!!Format!! .cvs with separator = “;” and decimal = “.” Samples in column, genes in row (use Gene Symbol as gene ID). If you want to use your own dataset during the course, please use the same csv format (separator = “;” and decimal = “.”).

Omic type : transcriptome

Normalized counts (linear scale)

FPKM (linear scale)