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Single cell RNA sequencing data analysis


​The aim of this workshop is to provide participants with the skills to perform basic analysis of scRNA-Seq data in order to identify cellular sub-populations and their marker genes.

Topics include

  • Short overview of the single cell RNA-Seq data
  • Preprocessing of 10x data (cellranger pipeline)
  • Filtering and normalization of data (Seurat)
  • Dimensionality reduction and visualization using tSNE (Seurat)
  • Partitioning cells into cluster and identification of cluster specific marker genes (Seurat)
  • Creation of lineage trajectories aka pseudotime analysis (Monocle)
  • Merging different datasets using CCA (Seurat)
  • Moving data between libraries and from/to Python

The detailed schedule will be distributed to accepted participants prior to the start of the workshop.

Number of participants


Entry requirements

  • Participants are expected to use their own computers.
  • Basic R knowledge, general Linux usage

This workshop is organised by the Research School in Stem Cell Biology in collaboration with the StemTherapy Bioinformatics Core Facility. Please be aware that the number of participants is limited. Participation in the workshop is free of charge for members of the Research School in Stem Cell Biology.

Page Manager:


February 12, 2019 at 9.00 - 17.00

Venue: BMC I1308


Parashar Dhapola
PhD student, Stem Cells and Leukemia Lab

Email: Parashar [dot] Dhapola [at] med [dot] lu [dot] se


Shamit Soneji
StemTherapy Bioinformatics Core Facility

Email: Shamit [dot] Soneji [at] med [dot] lu [dot] se

Stefan Lang
StemTherapy Bioinformatics Core Facility

Email: Stefan [dot] Lang [at] med [dot] lu [dot] se


Applications will open on November 14, 2018 and will run until December 5, 2018.

Applicants will be informed of the outcome of their application via email within one week after the application deadline.