This tool has been merged into the VIPER RNA-seq pipeline as a module to analysis immunology information. Thus this repository is deprecated now.
If you are using Linux or sshed into a Linux system:
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh
If you are using Mac locally:
wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh bash Miniconda3-latest-MacOSX-x86_64.sh
Follow the commands listed on screen, press the enter key to scroll down. Make sure to answer yes when asked if you want to prepend Miniconda3 to PATH.
Close your terminal, open a new one and you should now have Conda working! Test by entering:
conda update conda
You may need to add channels for convenience
conda config --add channels r
git clone https://github.com/hanfeisun/TIMER conda env create -f TIMER/environment.yml
Activate the TIMER conda environment
source activate timer
If you want to deactivate the TIMER enviroment, type
Download the reference expression data of immune cells and the marker immune gene in different cancer types.
This tool has been integrated into VIPER pipeline. See the usage at VIPER's page.
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