Single-Cell RNAseq Bioinformatics 2024

The course will consist of a mixture of conceptual and methodological lectures and hands-on bioinformatics sessions, including best practice and tips as learned first-hand by Earlham Institute’s faculty.

Participants will gain first-hand experience by learning how to assess data quality with the guidance of the faculty, troubleshoot small problems, and review the results. Hands-on sessions will be using data generated using both Smartseq2 and 10X protocols, from both short read and long read platforms.

There will be plenty of opportunities to ask questions, and a dedicated group discussion with other participants and the course trainers.

What will I learn?

• Understand the different data generated in scRNAseq experiments and analyses
• Learn how to assess data quality and optimise experimental design
• Hands-on experience in available tools and resources for analysing and visualising single-cell data
• Introduction to cell type identification, differential expression and pseudotime analyses
• Introduction to long read sequencing with application to transcript annotation and quantification in single cell research
• Overview of spatial transcriptomics platforms and demonstration of visualiser software capabilities

Pre-requisites

• You should have familiarity with the command line and be familiar with actions as in the Software Carpentry lesson on The Unix Shell.
• You should also have basic experience with R, such as being able to complete activities as they appear in Software Carpentry lesson Programming with R.
• Once accepted, participants should watch the following supportive course materials:
  • Introduction to data management video
  • ELIXIR Research Data Management materials (RDMbites)

Application process 

Please complete the application form to apply for a place on the training course. 

We aim to respond to your application within 2 weeks but will let you know if there is to be a delay. 

If successful and are offered a place for the course, you will be sent the link to complete registration, including payment options.
 

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