Useful code is a personal collection of R, Python, and Quarto notebooks for bioinformatics analyses. Most started in real projects and were later cleaned up so the useful parts were easier to find and reuse.

Browse the live catalog for method families and direct notebook links. Open the GitHub repository for the notebook files and their current parameters.

Personal research code

These notebooks are maintained as a personal analytical cookbook and are provided as-is. They may contain project-specific assumptions, thresholds, package APIs, or methodological choices that are not automatically appropriate for another dataset or study design.

Review each notebook, verify current upstream documentation, adapt the parameters and paths, and independently validate the workflow and outputs before relying on them. The scripts are not intended for clinical, diagnostic, or other high-stakes decision-making. No warranty is provided beyond the terms of the repository’s MIT License.

Templates and examples

templates/ contains the generalized notebooks. examples/ contains project-specific analyses and worked context. The catalog links to the files on GitHub so you can view or download them.

Template labels

  • SOURCE-BACKED WORKFLOW means a substantial implementation was available in the repository sources.
  • API / TUTORIAL REMINDER means a concise reminder based on a current package interface where no complete source workflow was found.
  • draft, validated, and blocked describe strict notebook validation status. SOURCE-BACKED does not mean scientifically validated everywhere, and draft does not mean broken.

Conventions

R analytical objects use .qs2, Python AnnData uses .h5ad, human-readable tables use TSV, and MOFA2 models use native HDF5 as an intentional exception.

License

See the repository README, archive, and LICENSE on GitHub.