This is a collection of analysis scripts that were used in our manuscript "Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis".
- The raw and interemediary input data files are hosted on Zenodo: DOI 10.5281/zenodo.1320734
- R 3.5
- Matlab R2015_b
- 01_prepare_scrnaseq_data - R: Preparation of the scRNAseq data
- 02_Seurat_processing - R: Processing of the scRNAseq data
- 03_matlab_zonation_reconstruction - Matlab: spatial reconstruction
- 04_scRNAseq_plots - R: tSNE plots
- 05_annotation_files - R: Ensembl annotation
- 06_zonation_plots - R: Zonation plots
- 07_rnaseq_germfree_antibiotics - R: Germfree and antibiotic analysis
- 08_pseudotime - R: pseudotime analysis