Single Cell Transcriptomics Workshop

Slides

Day 1

Introduction to Single Cell Transcriptomics

Data Processing

Days 2 & 3

Single Cell RNA-Seq Analysis Tools

Installing & Configuring Mamba

Starting a Jupyter notebook

Single Cell RNA-Seq Analysis

Getting Workshop Code

Code for the workshop can be downloaded from https://github.com/CBC-UCONN/Single-Cell-Transcriptomics/releases.

Copy the url for the version you wish to download and use wget or curl to download it.

To download the most recent version:

wget https://github.com/CBC-UCONN/Single-Cell-Transcriptomics/archive/refs/tags/2025.06.zip

One downloaded, unzip the file:

unzip 2025.06.zip

If you do not wish to run the entire pipeline (scripts 01-05), you will need to create symlinks to the pre-existing results files.

Within the Single-Cell-Transcriptomics directory, run the following commands to create the necessary symlinks:

ln -s /core/cbc/tutorials/workshopdirs/Single-Cell-Transcriptomics/leukemia/results/ leukemia/results