This repository contains analysis performed for the Single Cell Bioinformatics course at Saarland University.
- R
- Seurat
- CellChat
- tidyverse
10X Genomics Visium spatial transcriptomics dataset of mouse brain tissue.
- Data loading using Seurat
- Quality control and filtering
- Normalization using SCTransform
- PCA dimensionality reduction
- UMAP visualization
- Spatial clustering
- Identification of spatially variable genes
- Cell type annotation using label transfer
- Spatial cell-cell communication analysis
Sakshi Parate
MS Bioinformatics – Saarland University