SingleCell_Analysis_Scripts

This repository contains R/Python scripts for the analysis of scRNAseq and spatial transcriptomics

scRNA-seq analysis

Inside the scRNAseq folder, the scripts covering the following analysis steps using Seurat V5:

1. Quality control: removal of low quality cells based on mitochondrial percentage reads, removal of doublets with DoubletFinder
2. Normalization
3. Integration
4. Clustering
5. Differential abundance with MiloR
6. Postclustering analysis: Differential gene expression (for celltype marker), gene set enrichment, differential gene expression between 2 conditions, gene set enrichment.
7. Cell-cell interaction: MultinicheNet
8. Trajectory inference: Pseudotime with palantir, CellRank, RNA velocity using dynamical modeling with scvelo
9. Gene regulatory Networks: pySCENIC

Spatial Transcriptomics analysis

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)

References