A genome browser in your Jupyter notebook

pip install genomenotebook

New versions of genomenotebook are released on a regular basis. Make sure to upgrade your installation to enjoy all the features.

pip install genomenotebook --upgrade

Create a simple genome browser with a search bar. The sequence appears when zooming in.

Tracks can be added to visualize your favorite genomics data. See Examples for more !!!!

import genomenotebook as gn

g=gn.GenomeBrowser(gff_path=gff_path, fasta_path=fasta_path, init_pos=10000, bounds=(0,100000))
g.show()

https://dbikard.github.io/genomenotebook/

GenomeNotebook is developed using the nbdev framework, which makes it easy to develop Python packages with Jupyter Notebooks.

1. Navigate to the GenomeNotebook GitHub repository.

2. Click the “Fork” button in the top-right corner to create your own copy of the repository.

Clone your forked repository to your local machine by running the following command in your terminal: bash git clone https://github.com/dbikard/genomenotebook.git

Navigate to the cloned directory: bash cd genomenotebook

To keep your fork updated with the original repository:

Add the upstream repository: bash git remote add upstream https://github.com/dbikard/genomenotebook.git

Verify the remotes: bash git remote -v

You should see origin pointing to your fork and upstream pointing to the original repository.

1. Create a virtual environment and activate it

conda create -n gn python=3.11
conda activate gn

2. Install Required Tools

It is a good idea to read the nbdev Getting Started Guide and End-To-End Walkthrough

pip install jupyterlab
pip install nbdev
nbdev_install_quarto
pip install jupyterlab-quarto
nbdev_install_hooks

3. Install dependecies and genomenotebook in editable mode

pip install -e '.[dev]'

1. Sync with Upstream Repository Before making changes, ensure your fork is up-to-date:

git fetch upstream
git checkout main
git merge upstream/main

2. Create a New Branch

git checkout -b <feature-branch>

Replace with a descriptive name for your branch.

3. Make and Test Changes

Open the Jupyter Notebooks in the repository to make your changes. Changes should be made to notebooks in the nbs/ folder only. The package .py files are automatically generated from the notebooks.

Run the following command to rebuild the Python package, documentation and run the tests:

nbdev_prepare

4. When ready you can create a pull request.