Single-cell RNA-seq analysis

A full-day, in-person, hands-on workshop: you will work through a single-cell RNA-seq analysis on RCAC clusters using real data, with instructors in the room.

Workshop details

• Date: Thursday, October 29, 2026
• Format: Full day, hands-on
• Location: In person, West Lafayette (room details provided upon registration)
• Time: 8:30 AM – 4:30 PM EDT, with lunch 12:00 – 1:00 PM
• Registration: Register on luma
• Instructor: Arun Seetharam

Required before the workshop

Complete the lesson's Summary and Setup page before the workshop day. SSH access to the cluster and data staging must be done before the session starts.

Workshop materials

The workshop follows the lesson site Single-Cell RNA-Seq Analysis: Hands-on Training (Carpentries format, CC-BY 4.0). The lesson site is the canonical material for this workshop; this page does not duplicate it.

Prerequisites

• An RCAC cluster account and the ability to log in (HPC Orientation for Biologists)
• Basic Unix shell skills (HPC Exchange, Week 1)
• Comfort with basic R (R Skills for Biological Data)
• A laptop you can bring

What you will be able to do afterward

• Run R/RStudio and single-cell R packages on RCAC clusters (Installing R packages)
• Load, quality-filter, and normalize a single-cell count matrix
• Cluster cells, visualize embeddings, and export figures and tables for downstream use

Related guides

Background reading in the Life Sciences section:

• Installing R packages (includes the r-scrnaseq module)
• R Skills for Biological Data
• Publication-Quality Plots
• Running Bioinformatics Programs on RCAC

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