Intercept-MDS Single Cell Data Analysis Course - Valencia 2023

Introduction

Welcome to the Intercept-MDS Single Cell Data Analysis course, where we aim to provide you with a strong foundation in the principles of single-cell RNA-Seq data analysis. In today's research landscape, single-cell analysis stands as the preferred method for unravelling cellular heterogeneity. This course's primary objective is to equip you with the essential skills needed to effectively handle single-cell data, encompassing tasks such as preprocessing raw data, quantification, cell type clustering, and conducting differential gene expression and trajectory data analysis.

As we progress through this course, you will actively engage with the practical aspects of single-cell data analysis, gaining hands-on experience in processing and interpreting intricate datasets. This course serves as your entry point into the intricate world of single-cell data analysis, offering a valuable skill set that we hope will significantly enhance your academic pursuits and future research endeavours.

Things to do before the course

Your Course Team

Ángeles Arzalluz-Luque

Angeles began her academic journey by studying Biochemistry at the University of Córdoba. She completed her master's degree in Systems and Computational Biology at the University of Edinburgh in 2016.
Currently, she is in the final stages of her Ph.D. in Bioinformatics, with a specific focus on applying single-cell RNAseq and long-read sequencing techniques to investigate alternative isoforms. Her primary goal is to develop computational methods that simplify the analysis of scRNAseq data and enhance our understanding of single-cell biology.

Marta Benegas Coll

Marta holds a degree in Biotechnology from the Universitat Politècnica de València (UPV) and a master's degree in Bioinformatics from the Universitat Autònoma de Barcelona (UAB).

Since 2020, she has been a member of the Bioinformatics Team at BioBam, focusing on the development of user-friendly tools for the analysis of Single-Cell data. She is also an integral part of BioBam’s dedicated user support team.

Priyansh Srivastava

Priyansh studied bioinformatics at Amity University in India. Afterward, he was awarded the Max Arthur Macauliffe Scholarship and completed his master's degree in Bioinformatics at the National University of Galway, Ireland.

Since 2021, he has been a member of the BioBam team, where he is pursuing his industrial Ph.D. as part of the Intercept MDS network. He specializes in applying statistical models to scRNA-Seq data to derive functional insights.

Course Agenda

27th of September, 2023

Day 1 - Wednesday

Duration

Title

Teachers

9:00 -10:00

60min

Introduction to Single Cell Technologies

Ángeles Arzalluz-Luque

10:00 - 10:30

30min

Introduction to Single-Cell Data Analysis

Priyansh Srivastava

30 min

30 min

Coffee Break

11:00 - 11:45

45min

scRNA-Seq Quantification and Quality Check

Marta Benegas

11:45 - 13:00

1h 15min

Hands On 1: OmicsBox Intro, Quality Assessment and Quantification with OmicsBox

Marta Benegas & Priyansh Srivastava

13:00 - 14:30

30 min

Lunch

🥘

14:30 - 15:15

45min

Clustering, Preprocessing of the data and Clustering Visualization

Marta Benegas

15:15 - 16:00

45min

Differential Expression and Functional Enrichment Analysis

Marta Benegas

16:00 - 16:30

30 min

Coffee Break

16:30 - 18:00

1h 30min

Hands On 2: Data Preprocessing and Clustering, DEG and Enrichment with OmicsBox

Marta Benegas & Priyansh Srivastava

28th of September, 2023

Day 2 - Thrusday

Duration

Title

Teacher

9:00 - 9:45

30 min

R Packages for Single-Cell Analysis

Ángeles Arzalluz-Luque

9:45 - 10:30

60 min

Hands On 3: Single-cell Data Preparation and Clustering in R

Ángeles Arzalluz-Luque

30 min

Coffee Break

11:00 - 11:45

45min

Cell Type Annotation and Differential Abundance Analysis

Ángeles Arzalluz-Luque

11:45 - 13:00

1h 15min

Hands On 4: Cell Type-level Analysis in R

Ángeles Arzalluz-Luque

13:00 - 14:30

1h 30min

Lunch

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14:30 - 15:15

45min

Trajectory Analysis 1: Concepts, Tools & Applications

Priyansh Srivastava

15:15 - 16:00

45min

Trajectory Analysis 2: Pseudotime Inference

Priyansh Srivastava

16:00 - 16:30

Coffee

Coffee Break

16:30 - 18:00

1:30h

Hands On 5: Trajectory Analysis using Monocle3 (OmicsBox and R)

Priyansh Srivastava

29th of September, 2023

Day 3 - Friday

Duration

Title

Teacher

9:00 - 9:45

45min

Use-Case: Isoform Co-Expression Networks

Ángeles Arzalluz-Luque

9:45 - 10:30

45min

Cell-Cell Communication Analysis

Pau Badia (University of Heidelberg)

20 min

30 min

Coffee Break

10:50 - 11:35

45min

Demo on Cell to Cell Communications

Pau Badia (University of Heidelberg)

11:35 - 12:15

40min

Thesis Priyansh: scMasigPro

Priyansh Srivastava

12:15 - 13:50

45min

Computational methods for dissecting cancer heterogeneity

Joanna Ficek-Pascual (ETH Zürich)

13:00 - 14:15

1h 15min

Single Cell meets Real World: Intercept-MDS Use Cases Discussion

Network Contribution

14:30 - 17:00

Lunch at Albarcoa https://restaurantealbacora.com/

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