Workshop: Single Cell Data Analysis With Python

Wednesday 28 January | 16:10 - 17:40 | Workshop Room S15

Want to learn how to analyse single-cell data? Good at Python? Listen up!  

If you’re a Python coder and completely new to single-cell analysis, then this is for you! Whether you have a single-cell project on the horizon or simply want to expand your bioinformatics toolkit, this workshop will give you a solid foundation.  

In this hands-on workshop, we will introduce you to the Python ecosystem for single-cell, explain the analytical considerations for single-cell analysis, and showcase an end-to-end suggested processing workflow. We will explain how and why each step is done so that you leave with a conceptual understanding.

Daniel SnellHubert Slawinski from the Crick Genomics Platform will be around too for single cell chats about bench data generation and analysis.  

Image of dna and a scientist

Why Attend

Learning objectives

  • Explore and manipulate single-cell data using Scanpy and  Anndata.  

  • Perform QC, data viz and exploratory analysis of single-cell data in Python. 

  • Annotate cell-types via atlas-based label transfer using Celltypist. 

  • Understand scvi-tools ecosystem. 

  • Identify and evaluate key decision points and considerations (eg, cell cycle regression, doublet detection, sample integration). 

Who should attend

  • You should have 3+ years of Python experience (comfortable with Python (functions, pandas/numpy, debugging independently). 

  • Prior sc-RNAseq experience NOT required.   

  • Working Laptop with Python installed. 

  • A virtual env set up (uv, conda) and ready, if you would like to code along. 

What to expect

  • Warning: Due to the time limit on this workshop, if you attend without being proficient in Python, you will struggle to keep up.

  • There will not be time for debugging basic Python syntax during the workshop.

  • The main focus is on demystifying a single-cell analysis workflow using Python as the chosen language. 

Register your interest here

Please note places are limited and you will be informed if you were successful in securing your spot within three weeks.