About

A hands-on, three-day workshop on single-cell RNA-seq analysis for biologists who already write a little R and have used the command line. Run in person at the University of Oregon — no tests, no homework, no grades, just three days working through the modern scRNA-seq pipeline on your own laptop with the instructors beside you. The whole workshop runs on one laptop-friendly dataset (ifnb, ~24k cells, no 10x click-through): the core analysis modules (00–08) run in RStudio on your laptop Wednesday–Thursday, and the Friday-morning Talapas track (Modules 09–10) re-runs that same analysis on UO’s HPC cluster. An optional Day 0 the day before offers a refresher on laptop computer concepts & VS Code (P1) and R & the command line (P2) for anyone who wants it.

What you’ll do

Over three days you will work end-to-end through a standard scRNA-seq analysis:

  • Load a 10x Cell Ranger output into Seurat and inspect it
  • Run quality control (nCount, nFeature, percent.mt, doublets, ambient RNA)
  • Normalize, find highly-variable genes, scale, run PCA, build a neighbor graph, cluster, and embed with UMAP
  • Find cluster markers and assign cell-type labels by hand
  • Integrate multiple samples with Harmony / Seurat anchors and diagnose over-correction
  • Run condition-level pseudobulk differential expression with DESeq2
  • Run functional enrichment (GO, GSEA, Reactome) with clusterProfiler
  • Run differential abundance testing with miloR
  • Use reference-based annotation with Azimuth

The full Day-by-day plan is on the Schedule page.

Who this workshop is for

You will get the most out of this workshop if you:

  • Are a graduate student, postdoc, or researcher starting (or planning) a project that involves scRNA-seq
  • Can write basic R — read a CSV, use the tidyverse pipe |>, write a function, install a CRAN package
  • Have used a Unix command line at least a few times — cd, ls, grep, wget
  • Have a laptop with at least 16 GB RAM and ~10 GB free disk

If you have no R experience or your command-line skills are rusty, plan to attend the optional Day 0, and skim:

Instructors

Bill Cresko University of Oregon — Knight Campus and Institute of Ecology and Evolution —
Shannon Snyder University of Oregon — Biology Department and Institute of Ecology and Evolution —

Location & dates

Location Conference room, Knight Campus Building 2, University of Oregon
Tuesday, June 9 — optional Day 0 10:00 am – 12:00 pm or 3:00 – 5:00 pm; attend only one
Wednesday, June 10 — Day 1 10:00 am – 12:00 pm and 2:00 – 4:00 pm
Thursday, June 11 — Day 2 10:00 am – 12:00 pm and 2:00 – 4:00 pm
Friday, June 12 — Day 3 10:00 am – 12:00 pm, then a working lunch (food provided) 12:00 – 1:30 pm

See the Schedule page for the session-by-session plan.

What you should do before Day 1

Run the Software Setup workflow on the laptop you intend to bring. It installs R, RStudio, every package the workshop uses, and the small workshop dataset. Plan 30–60 minutes the day before — not the morning of.

If something errors during setup, the FAQ documents the issues that come up most often. If you cannot resolve the install yourself, the optional Day 0 session is the right place to bring it.

A resource you keep — learning beyond the workshop

This site is built to outlast the three days in the room. Everything here stays online and free after the workshop ends, so you can use it as a reference and a practice space as you begin applying scRNA-seq to your own data:

  • Re-run every tutorial at your own pace. The hands-on tutorials (01–08) and their long-form chapters stay available — come back to any step when you hit it in a real analysis.
  • Go further with the bonus tracks. WGCNA, trajectory inference & cell–cell communication, scATAC-seq analysis, spatial transcriptomics, and FAIR data sharing (Modules 13–17) — plus the upstream raw-data Cell Ranger pipelines (Modules 11–12) — are self-paced modules you can work through whenever you’re ready.
  • Scale up on Talapas. The Friday Talapas track (Modules 09–10) shows how to move the same analysis onto UO’s HPC; come back to it on your own time.
  • Look things up. The Glossary, prerequisite appendices, Additional Resources, and FAQ are meant to be returned to long after the workshop is over.

Bookmark the site and treat it as a living reference — we expect you’ll get as much out of it in the months after the workshop as during it.

Code of conduct & accessibility

  • Code of Conduct — applies to all workshop spaces (in-person and on the workshop’s GitHub repository). Reports go to the instructors.
  • Accessibility statement — what we currently provide and how to request additional accommodations. Please email at least one week before the workshop if you need an accommodation.

License & citation

Workshop source is released under the MIT License; lecture slides and figures are under CC BY 4.0 — adapt freely with attribution. If this workshop helps you learn scRNA-seq for a project that gets published, please cite:

Cresko, W. A., and Snyder, S. (2026). Single Cell RNA-seq Workshop. University of Oregon. https://github.com/wcresko/scRNAseq_tutorial

A CITATION.cff file at the repo root provides a machine-readable version.

Acknowledgments

The hands-on tutorials build on:

  • Khushbu Patel’s YouTube Tutorials repo (DESeq2 primer, scATAC-seq, WGCNA worked examples)
  • The Satija lab’s Seurat tutorials (PBMC 3k, integration, spatial)
  • The Sengupta lab’s scNotebooks — the LatinCells / Human Cell Atlas / Wellcome Connecting Sciences curriculum we cross-reference throughout
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