Bioinformatiha25 Tutorial on Intercellular signaling in Single Cell RNA

Here you will find all the materials and instructions needed to follow the hands-on sessions.
This tutorial will use two main analysis packages to meet different user preferences and levels of proficiency: a Python-package, i.e. CellPhoneDB, and a R package, i.e. scSeqComm! You may choose to work in either Python or R, depending on your background .

⚙️ Setup Instructions (Before the Tutorial)

To participate in the hands-on sessions, you will need to set up your environment and download the required materials in advance.

📥 Installation

•  Python-based analysis: Install the CellPhoneDB package by following the official documentation:
  https://cellphonedb.readthedocs.io/en/latest/
• R-based analysis: Install the Seurat and scSeqComm packages by following their installation guides:
  • Seurat https://satijalab.org/seurat/articles/install.html
  • scSeqComm https://gitlab.com/sysbiobig/scseqcomm

⚠️ Installing all the packages is not mandatory — you can use the language you prefer, or simply follow along using the provided pre-rendered HTML walkthroughs if you do not wish to run code locally.

📁 Download the Tutorial Materials

Download all tutorial materials from the shared repository folder. This includes: a Jupyter notebook (CellPhone.ipynb), a R Markdown script (scSeqComm.Rmd), the datasets (.h5ad for Python and .rds for R) and pre-rendered HTML versions of the tutorials.