Workshop in single-cell RNA-Sequencing Analysis

Welcome to the workshop that walks you through the standard analysis perfomed on single-cell RNA-Sequencing (scRNA-Seq) data.

Workshop Structure

The workshop is designed around 3 sessions, each of which lasts for ~50 minutes. The structure is the following.

1. Introduction
   • Theory: Short introduction to single-cell transcriptomics (~5 mins).
2. Session A
   • Theory: Pre-processing & HVGs detection (~15 mins).
   • Hands-on: Pre-processing & HVGs detection (~35 mins).
3. Session B
   • Theory: Dimensionality reduction & clustering (~15 mins).
   • Hands-on: Dimensionality reduction & clustering (~35 mins).
4. Session C
   • Theory: Cell type annotation (~15 mins).
   • Hands-on: Cell type annotation (~35 mins).
5. Q & A
   • Theory: Closing remarks (~10 mins).

File Sructure

session_a/
├── session_a.ipynb         # Jupyter notebook with code for pre-processing and HVGs detection
├── pbmc.csv.gz             # Raw counts expression matrix
├── annotation.csv.gz       # Table with annotation information
session_b/
├── pbmc.metadata.txt.gz    # Ground-truth cell labels
├── session_b.ipynb         # Jupyter notebook with code for dimensionality reduction and clustering
session_c/
├── session_c.ipynb         # Jupyter notebook with code for cell type annotation
├── sctype.csv              # Table with marker gene lists
├── mapping.csv             # Table with gene symbol to Ensembl gene id mapping
slides/
├── scRNA-seq_analysis.pdf  # Workshop slides
env.yml                     # Conda environment
requirements.txt            # List of dependencies

Dependencies Installation

All dependencies are listed within requirements.txt.

Installing dependencies with pip

In case you are working on an environment that already has Python installed, open a terminal and execute the following command.

pip install -r requirements.txt

Working with conda

In case you are using conda to manage environments, open a terminal and execute the following command.

conda env create --file env.yml

Contact

Authors

• Haris Manousaki (0009-0001-1356-2710), Information Management Systems Institute, Athena Research Center, Hellenic Republic

• Charis Sinnis (0000-0001-6231-0299), Information Management Systems Institute, Athena Research Center, Hellenic Republic

• George Georgakilas (0000-0003-1160-5753), Information Management Systems Institute, Athena Research Center, Hellenic Republic