GSCN workshop 2024

GSCN workshop 2024#

This repository is a collection of tutorials presented during the GSCN workshop 2024 ‘Computational single cell genomics for stem cell biologists’ - November 7-8, 2024.

The corresponding Jupyter Book is rendered here.

Table of Contents#

Material#

The data for each session can be found here.
Material for the workshop has been adapted from the single-cell best practices book, a live project from the Theis lab.
Recordings of previous single-cell RNA seq data analysis workshops can be found here.

Session-1#

  1. Preprocessing and Quality Control (QC)

  2. Data normalization

Session-2#

  1. Dimensionality reduction

  2. Clustering and annotation

  3. DGE

Session-3#

  1. Trajectory analysis

  2. Multisample analysis

Session-4#

  1. Introduction to spatial transcriptomics

Acknowledments#

Special thanks to the scverse community (especially the developers and the maintainers of scanpy and squidpy packages) and all the Theis lab for valuable contributions.
Huge thanks also go to Roshan Sharma from Dana Pe’er’s lab for kindly providing material for the workshop.