README for TIMER (0.1)

Introduction

TIMER is a tool for systematical evaluations of the clinical impact of different immune cells in diverse cancer types. The Web interface can be accesses here. The approach can be found in this paper.

Note

This tool has been merged into the VIPER RNA-seq pipeline as a module to analysis immunology information. Thus this repository is deprecated now.

Install

STEP 1: Installing Miniconda3 if you don't have conda installed

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

STEP 2: Get TIMER source code from github, and create TIMER env

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

source deactivate

STEP 3: Download the data for TIMER

Download the reference expression data of immune cells and the marker immune gene in different cancer types.

https://www.dropbox.com/s/qiwcfdnx1xp90j8/prec.zip?dl=0

STEP 4: Test if the tool works well

Type:

make test

Usage

This tool has been integrated into VIPER pipeline. See the usage at VIPER's page.