Home

Welcome to the UCL_CI_Single_Cell wiki!

This wiki expolores the major steps of scRNAseq (or similar single-cell -omics) analyses. This is intended to be a way to enhance the conventional scRNAseq workflow described out in the Seurat or scanpy tutorials, as discussed in Luecken and Theis (2019). This is only meant to be read as a rough guideline, providing tips and suggesting articles to help expand or enhance custom analysis pipelines.

Several other in-depth articles examining scRNAseq analysis:

• Bioconductor OSCA (R)
• NBI Sweden Tutorials (R and Python)
• Babraham Institute Bioinformatics Tutorials

Analysis Steps

• Preprocessing
• Quality Control
• Clustering
• Integration and Batch Correction (WIP)
• Phenotyping (WIP)
• Differential Expression
• Differential Abundance
• Cell-cell Communication (WIP)
• Single-cell Immune Receptors (TCR, BCR) (WIP)

Cell Type-specific Analysis

• T cells
• Myeloid cells (WIP)
• Tumour cells (WIP)

Kane Foster (30-05-2022)