IC-123 🔬

Data and script for processing IC-123

Overview

This repository contains data and scripts for analyzing IC-123.

Any data accompanying this project can be stored in the data/ directory, while any scripts used to process the data can be stored in the scripts/ directory.

Note

By default, any data or files added to the data/ directory are ignored by git due to our .gitignore, so you can store large files or data here without worrying about them being uploaded to Github. If you would to upload a small data file (<5MB) to Github, you can stage the file using force, -f, option to the git add:

# Stage file for commit
git add -f data/counts.tsv
# Commit the file to history
git commit -m "Adding small counts matrix"

Installation

To install the repository locally, you can use the following command:

# Clone the github repository
# and change your working directory
git clone https://github.com/OpenOmics/IC-123.git
cd IC-123/

Setup your environment

To setup your environment and download any missing packages, you can use the following command:

# Install any missing or 
# required python packages
# in a virtual environment
python -m venv .venv
source .venv/bin/activate
pip install -U pip
pip install -r requirements.txt

# Install any missing R packages
./packages.R