![Cover Image for Single Cell Basics: A 2-Day Hands-On scRNA-seq Workshop for Beginners [Registration for both days]](https://images.lumacdn.com/cdn-cgi/image/format=auto,fit=cover,dpr=2,background=white,quality=75,width=400,height=400/event-covers/z0/cb2509f2-8ec0-4695-88b4-892947bc9b7e.png)
Single Cell Basics: A 2-Day Hands-On scRNA-seq Workshop for Beginners [Registration for both days]
Have you read single-cell RNA-seq papers but never run the analysis yourself? This beginner-friendly workshop will give you a chance to explore a single cell dataset hands-on with your own dedicated virtual machine. We will go from a single cell counts object through cell type assignment and differential gene expression analysis.
Hosted by Boston Women in Bioinformatics (BWiB) and sponsored by Sprout Informatics, this 2-day live Zoom series is designed for students and early-stage researchers ready to get hands-on with single-cell analysis.
What you’ll do:
Understand how single-cell RNA-seq experiments work
Work with a 10X Genomics single cell dataset
Perform quality control (UMIs, gene counts, mitochondrial %)
Normalize and cluster cells
Identify marker genes
Determine the most abundant cell type — and explain why
What we’ll provide:
A dedicated cloud environment with all required packages pre-installed and data pre-downloaded
Instruction on how to connect via VS Code and run the analysis in a Jupyter notebook
Git repo with markdown files and step-by-step instructions
Day 1 — April 2
Understanding the experiment, connecting it to the gene-by-cell count matrix, setting up the analysis environment, and performing QC and filtering.
Day 2 — April 3
From clean data to biological insight: normalization, dimensionality reduction (PCA/UMAP), clustering, marker gene analysis, and assigning cell identities.
By the end of the workshop, you will have a solid grasp of how to manipulate a single cell object in R, and how to execute key single cell analyses.
**All participants in Day 1 will automatically be sent a meeting invite for Day 2**
Who is this for?
Beginners to scRNA-seq
Students looking for structured, hands-on training
Researchers who want to move from theory to practice
Summary
Format: Live on Zoom
Registration: $5 — all proceeds go directly to support BWIB!
Spots may be limited due to compute capacity