e-learning
Inferring single cell trajectories with Scanpy
Abstract
You've done all the hard work of preparing a single-cell matrix, processing it, plotting it, interpreting it, and finding lots of lovely genes. Now you want to infer trajectories, or relationships between cells... you can do that here, using the Galaxy interface, or head over to the Jupyter notebook version of this tutorial to learn how to perform the same analysis using Python.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How can I infer lineage relationships between single cells based on their RNA, without a time series?
Learning Objectives
- Execute multiple plotting methods designed to identify lineage relationships between cells
- Interpret these plots
Licence: Creative Commons Attribution 4.0 International
Keywords: 10x, MIGHTS, Single Cell, paper-replication
Target audience: Students
Resource type: e-learning
Version: 11
Status: Active
Prerequisites:
- Combining single cell datasets after pre-processing
- Filter, plot and explore single-cell RNA-seq data with Scanpy
- Generating a single cell matrix using Alevin
- Introduction to Galaxy Analyses
Learning objectives:
- Execute multiple plotting methods designed to identify lineage relationships between cells
- Interpret these plots
Date modified: 2025-01-14
Date published: 2023-12-08
Contributors: Björn Grüning, Helena Rasche, Marisa Loach, Mehmet Tekman, Pavankumar Videm, Saskia Hiltemann, Wendi Bacon
Activity log
