scRNA-seq bioinformatics
Trainers: Cecilia Dominguez Conde and Rasa Elemtaite
Overview: This hands-on session will be split into two parts, and will give you the chance to analyse different single cell RNA sequencing data objects.
Learning outcome
By the end of this session you will be able to:
- Perform quality control and data normalisation
- Perform dimensionality reduction (PCA, UMAP) and clustering
- Perform batch correction using BBKNN
- Use automated cell type annotation (CellTypist)
- Prepare data for the use with different tools (CellphoneDB)
- Read and explore single-cell VDJ data contained in contig annotation files
- Integrate single-cell RNA expression and single-cell VDJ data
- Quality control and interpretation of scTCR-seq data based TCR chain combinations detected
- Determine the usage of V(D)J gene segments across cell types and cell states
- Identify clonotypes using several parameters, determine clonal expansion and repertoire overlap across conditions
Materials: