Appendix A — Contributors & acknowledgments
This book is the work of many hands, and it stands on a great deal of generously shared material. Individual chapters carry their own author bylines; this page is the single place that credits everyone — and every adapted source — across the whole book.
A.2 Third-party material and sources
A few figures, explanations, and screenshots come from others’ openly-licensed work. We are grateful to their authors; each item is used with attribution and retains its own license.
- Bioconductor GenomicRanges and SummarizedExperiment vignettes (Artistic-2.0) — explanatory passages in the Genomic ranges chapter and the SummarizedExperiment schematic (
se.png), credited in place. - scikit-learn (BSD 3-Clause) — the machine-learning overview figure.
- Tsompana & Buck (2014), Epigenetics & Chromatin (CC BY 4.0) — the chromatin- accessibility comparison figure in the ATAC-seq chapter.
- Wikimedia Commons contributors (CC BY-SA 3.0/4.0) and NIH BioArt (public domain) — figures in the Biology primer, credited in each caption.
- Microsoft VS Code documentation (CC BY 3.0 US) and Posit product screenshots (RStudio, Positron; used for identification only) — IDE screenshots.
The original content of this book is released under CC-BY 4.0. Third-party material is openly licensed (CC-BY family, BSD, or public domain) or used as fair-use product screenshots, and is attributed where it appears; so the book is uniformly open. See the publication-readiness plan for the provenance cleanup history.
A.3 Datasets
The book reuses several published datasets, cited in the chapters that use them — among them the palmerpenguins data (CC0) and msleep (bundled with ggplot2) used in the tidyverse chapters, the DeRisi et al. (1997) diauxic-shift time course, the airway RNA-seq dataset (Himes et al.), GEO accession GSE103512, ENCODE CTCF peaks (ENCFF960ZGP), a DNA-methylation dataset from a Galaxy Training Network tutorial (CC BY 4.0), and curated microbiome and single-cell datasets from Bioconductor data packages. Datasets we redistribute are vendored under data/; figure sources are recorded in images/README.md.
A.4 Tools
Built with Quarto, R, and Bioconductor, and published openly so others can read, reuse, and contribute.
A.5 Contributing
Corrections, suggestions, and contributions are welcome through the GitHub repository — open an issue or a pull request. If you contribute material, you’ll be credited here and in the relevant chapter.