Single cell RNA-seq data analysis with R

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About

This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE project.

Schedule

Date

27.05.2019 - 29.05.2019

Location

The event is organised at the CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. The best way to reach us is by public transportation; more detailed travel tips are available here.

Prerequisities

In order to participate in this course you should have prior experience in using R.

Learning objectives

After this course you will be able to:

• use a range of bioinformatics tools to analyze single cell RNA-seq data
• discuss a variety of aspects of single cell RNA-seq data analysis
• understand the advantages and limitations of single cell RNA-seq data analysis

Programme

Monday 27.5.2019

• Introduction and experimental design (Åsa Björklund, Jules Gilet)
• QC, data preprocessing (Åsa Björklund)
• Normalisation and batch effect correction (Heli Pessa, Bishwa Ghimire)
• Data integration (CCA, MNN, dataset alignment) (Ahmed Mahfouz)

Tuesday 28.5.2019

• Dimensionality reduction (PCA, tSNE and UMAP) (Paulo Czarnewski)
• Clustering (Ahmed Mahfouz)
• Differential gene expression analysis (Ståle Nygård and Olga Dethlefsen)

Wednesday 29.5.2019

• Cell type identification (Philip Lijnzaad)
• Trajectories/Pseudo-time (Paulo Czarnewski)
• Spatial transcriptomics (Jeongbin Park and Lars Borm)

Lecturers

• Åsa Björklund (SciLifeLab, NBIS, Sweden)
• Paulo Czarnewski (SciLifeLab, NBIS, Sweden)
• Ahmed Mahfouz (LUMC, Netherlands)
• Ståle Nygård (UIO, Norway)
• Olga Dethlefsen (SciLifeLab, NBIS, Sweden)
• Jeongbin Park (Charité-Universitätsmedizin Berlin & de.NBI - German Network for Bioinformatics Infrastructure, Germany)
• Lars Borm (Karolinska Institutet, Sweden)
• Jules Gilet (Institut Curie, France)
• Heli Pessa (University of Helsinki, Finland)
• Bishwa Ghimire (FIMM, Finland)
• Philip Lijnzaad (Princess Maxima Center for Pediatric Oncology, Netherlands)

Additional information

• Content: [email protected]
• Practicalities: [email protected]