Introduction to Single-Cell Transcriptomics

• George Georgakilas (ΑΤΗΕΝΑ RC)

This introductory session provides an overview of single-cell RNA sequencing (scRNA-seq), the Scanpy ecosystem, and the main objectives of the workshop.

Pre-processing & HVGs Detection

• Charis Sinnis (ATHENA RC)

This theoretical session introduces quality control, highlighting key factors to consider when defining QC thresholds. It also covers preprocessing strategies and highly variable gene (HVG) selection, explaining their importance in capturing biological variability and the computational approaches used to identify them.

Hands-on 1: Pre-processing & HVGs Detection

• Charis Sinnis (ATHENA RC)

This hands-on session guides participants through preprocessing and HVG selection, emphasizing important data characteristics and their influence on analytical decisions.

Dimensionality Reduction & Clustering

• Haris Manousaki (ATHENA RC)

This theoretical session introduces dimensionality reduction and clustering methods, explaining their underlying principles and their role in identifying cellular populations and exploring transcriptomic heterogeneity.

Hands-on 2: Dimensionality Reduction & Clustering

• Haris Manousaki (ATHENA RC)

This hands-on session focuses on principal component analysis (PCA), dimensionality reduction, and clustering, with particular emphasis on parameter selection and its impact on downstream results.

Cell Type Annotation

• George Georgakilas (ΑΤΗΕΝΑ RC)

This theoretical session introduces differential gene expression analysis for identifying cluster-specific marker genes. It also discusses cell-type annotation strategies, their underlying assumptions, and common challenges and pitfalls.

Hands-on 3: Cell Type Annotation

• George Georgakilas (ΑΤΗΕΝΑ RC)

This hands-on session guides participants through cell-type annotation using differentially expressed genes, known cell-type markers, and an enrichment-based approach.

Closing remarks

• George Georgakilas (ΑΤΗΕΝΑ RC)

The workshop concludes with an open discussion addressing participants' questions, coding issues, and common troubleshooting challenges encountered during the hands-on sessions.