immunoduct

Pipeline for tumor immunology. Input should be GCT files made by riboduct.

Installation

1. Install conda

immunoduct requires conda package manager. To install conda for Linux,

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

2. Install pipeline

Download and install immunoduct.

git clone https://github.com/msfuji/immunoduct.git
cd immunoduct
# activate conda
eval "$($HOME/miniconda3/bin/conda shell.bash hook)"
conda install mamba -c conda-forge
bash immunoduct.sh install
conda deactivate

3. Install R packages

Install required R packages. This will install ESTIMATE, xCell, EPIC, and MCPcounter for immune profiling, along with others. In SHIROKANE, you may use /usr/local/package/r/3.6.0/bin/Rscript.

Rscript scripts/install_r_packages.R

CIBERSORT is not automatically installed because of its license. It should be noted that immunoduct runs without CIBERSORT. If you still want to use CIBERSORT, you may go to https://cibersort.stanford.edu/ and request R source code. Download CIBERSORT.R, LM22.txt, and place them in scripts/.

Usage

Make a local copy of pipeline for each project.

git clone https://github.com/msfuji/immunoduct.git
cd immunoduct

Modify config.yaml. Start running the pipeline.

eval "$($HOME/miniconda3/bin/conda shell.bash hook)"
conda activate immunoduct
bash immunoduct.sh run config.yaml
conda deactivate
conda deactivate

The output is saved to output/immunoduct.gct.

Visualization (Optional)

eval "$($HOME/miniconda3/bin/conda shell.bash hook)"
conda activate immunoduct

# install clustergrammer (run only once)
pip install clustergrammer_widget
jupyter nbextension enable --py --sys-prefix widgetsnbextension
jupyter nbextension enable --py --sys-prefix clustergrammer_widget

bash immunoduct.sh view
conda deactivate
conda deactivate