Schedule
The workshop runs over three days at Knight Campus Building 2, University of Oregon — Wednesday–Friday, June 10–12, 2026 — with an optional Day 0 the day before (Tuesday, June 9). The day-by-day plan is below; every session’s lecture, reading, tutorial, and Talapas script lives on the Materials page.
What to bring
- Your own laptop with at least 16 GB RAM and ~10 GB free disk — the workshop is hands-on and there are no lab machines
- R ≥ 4.4 and RStudio Desktop installed (see Software Setup)
- The workshop packages installed ahead of time (covered in Module 00; see Software Setup)
- A power adapter — outlets are limited in the conference room
Day 0 (optional) — Computational Refresher
Offered on Tuesday, June 9 (same room) as two identical 2-hour sessions — 10:00 am – 12:00 pm and 3:00 – 5:00 pm. You only need to attend one; come to whichever fits your schedule. Bring your laptop and any install problems you couldn’t solve on your own. Each session is two prerequisite modules — lecture, reading, and a hands-on tutorial for each are on the Materials page:
| Block | Session |
|---|---|
| Hour 1 (10:00–11:00 / 3:00–4:00) | Module P1 — Computer Systems & the Command Line (computers & OS, VS Code locally, the shell) |
| Hour 2 (11:00–12:00 / 4:00–5:00) | Module P2 — R & RStudio (R language, data structures, the tidyverse, reading/writing data) |
Can’t make Day 0? It’s optional, but if you’re new to the command line or R, work through the two P1 & P2 readings and the Software Setup before Day 1. (Connecting to Talapas with VS Code Remote-SSH is covered in Module 09 on Friday — not a Day 0 prerequisite.)
Day 1 — Wednesday, June 10 · Foundations, QC, and Clustering
10:00 am – 12:00 pm and 2:00 – 4:00 pm.
| Block | Session |
|---|---|
| 10:00 – 10:15 | Welcome & workshop overview |
| 10:15 – 11:30 | Doug Turnbull (Director, GC3F) — single-cell data generation technology |
| 11:30 – 12:00 | Module 00 — Get up and running with R, RStudio, Quarto & VS Code on your laptop |
| 2:00 – 3:00 | Module 01 — QC & preprocessing |
| 3:00 – 4:00 | Module 02 — Dimensionality reduction & clustering |
Day 2 — Thursday, June 11 · Annotation, Integration & Downstream Analysis
10:00 am – 12:00 pm and 2:00 – 4:00 pm.
| Block | Session |
|---|---|
| 10:00 – 10:40 | Module 03 — Markers & manual annotation |
| 10:40 – 11:20 | Module 04 — Reference-based annotation |
| 11:20 – 12:00 | Module 05 — Multi-sample integration |
| 2:00 – 2:40 | Module 06 — Pseudobulk differential expression |
| 2:40 – 3:20 | Module 07 — Functional enrichment analysis |
| 3:20 – 4:00 | Module 08 — Differential abundance |
Day 3 — Friday, June 12 · Talapas HPC & Wrap-up
10:00 am – 12:00 pm, then a working lunch (food provided) 12:00 – 1:30 pm.
| Block | Session |
|---|---|
| 10:00 – 11:00 | Module 09 — VS Code & SLURM Basics on Talapas (connecting with VS Code Remote-SSH, interactive sessions, SLURM job submission) |
| 11:00 – 12:00 | Module 10 — running the analysis pipeline as batch SLURM jobs (the 01–08 R scripts) on Talapas |
| Working lunch 12:00 – 1:30 | Final questions, feedback, suggestions for improvement, and ideas for future workshops |
Bonus tracks — self-paced after the workshop
Beyond the three in-person days, the workshop ships a set of bonus modules (raw-data Cell Ranger pipelines and downstream analyses like WGCNA, trajectory, scATAC, spatial, and FAIR) for you to work through on your own time — see Materials → Bonus modules.
During-workshop support
The instructors will be in the room throughout the workshop. For questions outside workshop hours, email is the most reliable channel — see the About page.