About these guides

What they are

Open reference guides for analysing five common kinds of functional genomics data (bulk RNA-seq, ATAC-seq, ChIP-seq, Hi-C and single-cell RNA-seq), from raw reads to biological interpretation. Each guide pairs a reusable processing pipeline with worked R code, explains why each step is done the way it is, and states plainly what the results can and cannot show. An extension in every guide, and a shared appendix, cover comparisons across species.

The guides document one practitioner’s way of doing each analysis. They are not an authoritative standard or a formal course: other valid approaches exist, and settings should be adapted to your own data and checked against each tool’s documentation.

How they were checked

  • R code: every R block was executed with R 4.5 and Bioconductor 3.22 on public example data (airway, PBMC 3k, DiffBind’s tamoxifen set) or on synthetic files in the exact formats the pipelines write. The package versions are pinned in pipelines/envs/r_analysis.yaml.
  • Pipelines: the RNA-seq and ChIP/ATAC pipelines were run end to end on simulated data, and their results matched the simulated truth. The Hi-C, scRNA-seq and consensus-genome pipelines are dry-run tested. Every pipeline’s conda environment has been built from its file. No pipeline has been run on a full-size real dataset; reports from real runs are welcome.
  • Facts and thresholds: QC thresholds were checked against ENCODE’s published standards, tool options against each tool’s own documentation or source code, and references against PubMed.

Found a mistake? Please use the “Report an issue” link at the bottom of any page.

Example study

Several guides illustrate results with an openly available study of primate astrocyte evolution:

Ciuba K, Piotrowska A, Chaudhury D, et al. Molecular signature of primate astrocytes reveals pathways and regulatory changes contributing to human brain evolution. Cell Stem Cell 2025;32:426–444. doi:10.1016/j.stem.2024.12.011

Licence

These are open access materials. The guides and website content are distributed under the Creative Commons Attribution licence (CC BY 4.0), which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. The pipeline code is released under the MIT licence.

Acknowledgements

The guides were developed at:

Nencki Institute of Experimental Biology, Warsaw, Poland
Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland

The author thanks Aleksandra Pękowska, Katarzyna Ciuba, Aleksandra Piotrowska and Eryk Duński for their collaboration and support.

The page structure is inspired by the openly licensed training materials of the Harvard Chan Bioinformatics Core (HBC). Guides link to HBC lessons wherever those go deeper.

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