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Single Cell Basics:
A 2-Day Hands-On scRNA-seq Workshop for Beginner

Zoom
Ticket Cost: $5.00
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Have you read single-cell RNA-seq papers but never run the analysis yourself? This beginner-friendly workshop will take you from raw 10x Genomics data to identifying real biological cell types.

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
  • Load a real PBMC dataset from 10x Genomics
  • Perform quality control (UMIs, gene counts, mitochondrial %)
  • Normalize and cluster cells
  • Identify marker genes
  • Determine the most abundant cell type — and explain why

What will we 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 confidently interpret a UMAP and defend your biological conclusion.

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

Code of Conduct:

This event is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion (or lack thereof), or technology choices. We do not tolerate harassment in any form. Anyone violating these rules may be sanctioned or banned from attending at the discretion of the conference organizers. Please contact the organizers through lu.ma messaging/Slack, if you feel someone has broken the code of conduct.

Original source and credit: http://2012.jsconf.us/#/about & The Ada Initiative

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