gokit

gokit is a command-line toolkit for Gene Ontology (GO) enrichment analysis.

Quick Start

These lines represent the simplest method to rapidly install and run gokit.

# install
pip install gokit

# download default ontology files into current directory
gokit download

# run enrichment
gokit enrich \
  --study study.txt \
  --population population.txt \
  --assoc assoc.txt \
  --out results/goea

Below are more detailed instructions, including alternative installation methods.

1) Installation

To help ensure gokit can be installed using your favorite workflow, we have made gokit available from pip and source.

Install from pip

To install from pip, use the following commands:

# create virtual environment
python -m venv venv
# activate virtual environment
source venv/bin/activate
# install gokit
pip install gokit

Note: the virtual environment must be activated to use gokit.

Install from source

Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:

# download
git clone https://github.com/JLSteenwyk/gokit.git
cd gokit/
# create virtual environment
python -m venv venv
# activate virtual environment
source venv/bin/activate
# install
pip install -e .[dev,plot]

To deactivate your virtual environment, use the following command:

# deactivate virtual environment
deactivate

Note: the virtual environment must be activated to use gokit.

2) Usage

To use gokit, execute the following command:

gokit enrich \
  --study study.txt \
  --population population.txt \
  --assoc assoc.txt \
  --out results/goea