Installation

This handbook is a static documentation site. It does not need a server unless your browser blocks local file links.

Dependencies

To view the documentation, you only need a modern browser. To run the notebooks and scripts, install the language environments required by each protocol.

# Recommended optional environment for Python notebooks
conda create -n bioinformatics-handbook python=3.11 -y
conda activate bioinformatics-handbook
pip install jupyter pandas numpy matplotlib

# R workflows usually need Bioconductor/CRAN packages listed in each protocol page
install.packages(c("ggplot2", "dplyr", "readr"))
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

Open locally

Start from the docs front page:

notebook/docs/index.html

Or open the Jupyter notebook index:

notebook/INDEX.ipynb

Verification

The current package was verified by parsing generated HTML links and notebook JSON.

55 docs/front-door HTML files checked
0 missing local href/src references
48 .ipynb files parsed as valid notebook JSON