This series of Jupyter Notebooks contains executable "recipes" for bioinformatics workflows using scikit-bio.
Readers interested in gaining more background information on bioinformatics may want to start with An Introduction to Applied Bioinformatics, which makes extensive use of scikit-bio to teach concepts in bioinformatics.
This is not the main scikit-bio documentation. You can find the latest scikit-bio API documentation here.
These notebooks are only tested to work with scikit-bio 0.5.0, which requires Python 3.4 or later. The notebooks may not work with other versions of scikit-bio. Click here to view scikit-bio 0.5.0 API documentation.
There are two ways to read the scikit-bio cookbook.
The easiest way is to read the static online version.
The recommended way is to install the interactive version and read it locally. This will let you exectute and experiment with the recipes from within your web browser. To view and interact with the notebooks, you'll need Python 3.4 or later, scikit-bio 0.5.0, and the Jupyter Notebook installed.
The easiest and recommended way to install these dependencies is via the
conda package manager available in Anaconda or miniconda. Once you have
conda installed, create a new environment with the following packages:
conda create -c https://conda.anaconda.org/biocore -n scikit-bio-cookbook python=3.5 scikit-bio=0.5.0 jupyter requests
Activate the environment:
source activate scikit-bio-cookbook
Install extra (non-conda) dependencies needed for recipes:
pip install ete3 qiime-default-reference
Next, you'll need to download the scikit-bio cookbook. We recommend pulling the latest version from GitHub (you may need to install
git first), and then changing to the new directory that is created:
git clone https://github.com/biocore/scikit-bio-cookbook.git cd scikit-bio-cookbook
Finally, start the Jupyter Notebook server:
jupyter notebook Index.ipynb
# Ignore this code, it is necessary to display the table of contents below. from skbiocookbook import cookbook_toc from IPython.display import HTML HTML(cookbook_toc())