Single cell RNA sequencing analysis course

Scilifelab Solna, Rooms Air & Fire, 2018-05-21 - 2018-05-23

This course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include:

  • An overview of the current scRNAseq techniques
  • Basic overview of pipelines for processing raw reads into expression values
  • Quality control of scRNAseq data
  • Dimensionality reduction and clustering techniques
  • Data normalization
  • Differential gene expression for scRNAseq data
  • Examples on how to use these tools in a research project.
Schedule

Course schedule can be found here: Schedule

Exercises

All exercises for the afternoon sessions can be found at Exercises.

For working on Uppmax: to use the allocations we have for the course, please look here.

Precourse

Please read carefully the Precourse material before the course start.

Address and travel suggestions

Travel Info

Course leaders

Here are some useful links to tools, courses etc.

  • Single cell RNA-seq course at from Hemberg lab here
  • Repository listing many scRNA-seq tools here
  • SingleCellExperiment objects for many datasets here
  • Conquer datasets - many different datasets based on a salmon pipeline here
  • The Human Cell Atlas project here
  • The github repository for this course. Also contains the R markdown scripts that was used to generate all the exercises here
  • Bitbucket repository for QC report scripts here
  • Bitbucket repository for the NBIS scRNAseq pipeline here