---
title: "Intercept-MDS Single Cell Data Analysis Course - Valencia 2023"
canonical: "https://help.biobam.com/space/BTP/3307372599/Intercept-MDS%20Single%20Cell%20Data%20Analysis%20Course%20-%20Valencia%202023"
format: markdown
---
# Your Course Team

# Course Agenda

## 27<sup>th</sup> of September, 2023

| Day 1  - Wednesday | Duration | Title | Teachers |
| --- | --- | --- | --- |
| 9:00 -10:00 | 60min | [Introduction to Single Cell Technologies](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-1/introduction-to-single-cell-technologies/) | Ángeles Arzalluz-Luque |
| 10:00 - 10:30 | 30min | [Introduction to Single-Cell Data Analysis](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-1/introduction-to-scrna-seq-data-analysis/) | Priyansh Srivastava |
| 30 min | 30 min | Coffee Break | ☕ |
| 11:00 - 11:45 | 45min | [scRNA-Seq Quantification and Quality Check](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-1/single-cell-rna-seq-quantification-and-quality-check/) | Marta Benegas |
| 11:45 - 13:00 | 1h 15min | [Hands On 1: OmicsBox Intro, Quality Assessment and Quantification with OmicsBox](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-1/hands-on-session-1:-quantification,-qc,-and-preprocessing-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 ](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-1/clustering-&-umap/) | Marta Benegas |
| 15:15 - 16:00 | 45min | [Differential Expression and Functional Enrichment Analysis](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-1/differential-expression-+-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](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-1/hands-on-session-2:-data-preprocessing-and-clustering,-deg-and-enrichment-with-omicsbox/) | Marta Benegas & Priyansh Srivastava |

## 28<sup>th</sup> of September, 2023

|  |  |  |  |
| --- | --- | --- | --- |
| Day 2  - Thrusday | Duration | Title | Teacher |
| 9:00 - 9:45 | 30 min | [R Packages for Single-Cell Analysis](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-2/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](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-2/hands-on-session-3:-single-cell-data-preparation-and-clustering/) | Ángeles Arzalluz-Luque |
|  | 30 min | Coffee Break | ☕ |
| 11:00 - 11:45 | 45min | [Cell Type Annotation and Differential Abundance Analysis](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-2/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](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-2/hands-on-session-4:-cell-type-level-analysis-in-r/) | Ángeles Arzalluz-Luque |
| 13:00 - 14:30 | 1h 30min | Lunch | 🥘 |
| 14:30 - 15:15 | 45min | [Trajectory Analysis 1: Concepts, Tools & Applications](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-2/trajectory-analysis-1:-concepts-&-applications/) | Priyansh Srivastava |
| 15:15 - 16:00 | 45min | [Trajectory Analysis 2: Pseudotime Inference](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-2/trajectory-analysis-2:-tools-&-algorithms/) | 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)](https://training.biobam.com/intercept-mds-single-cell-data-analysis-course-valencia-2023/day-2/hands-on-5:-trajectory-inference-in-omicsbox/) | Priyansh Srivastava |

## 29<sup>th</sup> 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/](https://restaurantealbacora.com/) | 🥘 |