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Applied Single-Cell Bioinformatics, PhD


Technical University of Denmark


General course objectives:
After you have taken this course, you will be able to do state-of-the-art bioinformatics analysis of single-cell data. The main focus in the course is on single-cell RNA-sequencing but we will also cover both spatial and multimodal single-cell data.

Learning objectives:
A student who has met the objectives of the course will be able to:
  • independently seek out and obtain relevant information about single-cell data analysis.
  • list various single-cell technologies along with relevant biological use-cases.
  • discuss strengths and weaknesses for various single-cell technologies.
  • assess strengths and weaknesses with various experimental setups.
  • list various bioinformatic analysis tools and what they are used for.
  • discuss strengths, weaknesses, and key parameters for various analysis approaches.
  • apply and interpret state-of-the-art bioinformatic analysis to single-cell data in the biological context of the data.
  • use R to organize, modify, and visualize data.
  • as a group design and execute a single-cell analysis project.
  • clearly present obtained results orally using proper visual aids.

Contents:
The first part of the course will introduce and have you work with various single-cell technologies and analyses, including, but not limited to: • Single-cell RNA-seq • Dimensionality reduction, integration, clustering, and cell-type annotation • Downstream analysis such as differential expression and differential cell type abundance • Multimodal single-cell analysis • Spatial transcriptomics In the second half of the course, you will have to do a group-based project on real data. For this project, you can work on data we provide or bring your own data (e.g., from your master thesis or PhD project) as long as the dataset has been approved by a teacher.

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Course organizer
Kristoffer , Lars Rønn
Place/Venue
Anker Engelunds Vej 1
City
2800 Kgs. Lyngby
Country
Denmark
Workload
5
Link
http://kurser.dtu.dk/course/22172