Github repository for BrainOmics course 2024

This repository contains all the notebooks of the hands-on sessions that will be held during the BrainOmics 2.0 course at the Human Technopole in Milan, Italy from November 18 to 22, 2024.

Hands-on Sessions

Day 1: Essential Workflow for single-cell RNASeq computational analysis

• WalkThrough
• Notebook 1: from count matrix to clusters
• Notebook 2: cluster characterization
• Resources

Day 2: Advanced approaches to single-cell RNA-seq data

• WalkThrough
• Notebook 1: additional processing and metacells
• Notebook 2: Imputation and Trajectory inference
• Notebook 3: Trajectory analysis
• Notebook 4: Transcription factor activity prediction
• Resources

Day 3: Computational analysis of spatial transcriptomics data

• WalkThrough
• Spatial Transcriptomics notebook
• Resources

Course Project

• WalkThrough
• First Step
• Second Step

Contacts

• Cristina Cheroni
• Davide Castaldi
• Alessia Valenti
• Gaja Matassa