Bioinformatics scRNAseq analysis pipelines,
3-4 April 2025,
FORTH-IMBB, Heraklion.  

Bioinformatics partners from IRB Camille Attolini and Lidia Mateo visited IMBB a two day workshop with IMBB bioinformatics Ethan Baird and Vasiliki Theodorou. 

 

Aims of the workshop :

  1. Establish the pipeline/ adjust to IMBB cluster environment.
  2.  CM created  SCENTINEL Github account, granted access to LM, EB, VT 
  3.  Establish connectivity and accessibility of SCENTINEL IMBB data storage.  
  4.  Upload code from the 2-day workshop onto github 

    Detailed description of the pipeline: 

  1. Data was processed with the cellranger software from 10X genomics 
  2. Data was imported into R and a Seurat object created for each sample separately 
  3. Doublet score was computed using scDoubletFinder for each sample independently. Cells flagged as doublets were filtered out. 
  4. Cells were merged into a single object and expression was normalized using SCTransform 
  5. Cell cycle scores and Phase classification was performed using Seurat dedicated functions 
  6. Data was renormalized regressing out for cell cycle scores 
  7. PCA, UMAP and unsupervised clustering were computed in the resulting object 
  8. Descriptive plots were generated for fraction of cells per cluster and genotype
  9. RNASeq differentially expressed genes were projected into the single cell data in order to visualize commonalities