Getting Started

System Requirements

OS: linux, MacOS

R: https://www.r-project.org/

Python: >3.6

Clone repository to local

git clone https://github.com/CostaLab/scrna_seurat_pipeline.git

Dependent libraries installation

Rscript packages_install.R

Toy example

Run data producing

This step will take around 1 hour, depends on the hardware performance.

cd scrna_seurat_pipeline
cp conf/config.R conf/config_toy.R ## toy configuration file
cp run_example.sh run_toy.sh ## Please edit run_toy.sh to fit your environment
sh run_toy.sh toy

Run visualization

This step will take around 40 minutes, depends on the hardware performance.

cp run_viz_example.sh run_viz_toy.sh ## Please edit run_viz_toy.sh to fit your environment
sh run_viz_toy.sh toy

Check the report

Go to toy/report/, open index.html, you can check the result