scRNAseq analysis

Intro and docs

For a comprehensive understanding of scRNAseq data processing, check out these courses:

• Broad institute course

• Biocellgen group

Pipeline

For single-cell RNAseq analysis please use the nf-core/scrnaseq pipeline. We currently recommend running the cellranger tool as it’s the most requested one and currently compatible with our downstream analysis scripts.

For secondary analysis, we are currently just running custom R and Rmarkdown files using the Seurat library. Please ask your team leader for example scRNAseq projects.