This repository contains R/Python scripts for the analysis of scRNAseq and spatial transcriptomics
Inside the scRNAseq folder, the scripts covering the following analysis steps using Seurat V5:
- Quality control: removal of low quality cells based on mitochondrial percentage reads, removal of doublets with DoubletFinder
- Normalization
- Integration
- Clustering
- Differential abundance with MiloR
- Postclustering analysis: Differential gene expression (for celltype marker), gene set enrichment, differential gene expression between 2 conditions, gene set enrichment.
- Cell-cell interaction: MultinicheNet
- Trajectory inference: Pseudotime with palantir, CellRank, RNA velocity using dynamical modeling with scvelo
- Gene regulatory Networks: pySCENIC
Inside the spatial_transcriptomics folder, the scripts cover the following analysis steps using scanpy:
- Visium (spot resolution)
- Xenium (single-cell resolution)
- RESOLVE Biosciences (single-cell resolution)