Code and scripts used in the analysis of a comprehensive snRNAseq mouse cerebellar cortex atlas, as described in our recent publication.
Example scripts used for clustering and cell type annotation are available in annotation.
Markdown files to reproduce the main figures are available in main_figures and below:
Figure 1: Cerebellar cell type annotation
Figure 2: Characterization of spatial variation
Figure 3: Cross-cluster continuity of neuronal populations
Figure 4: Characterization of MLI2 cells
Figure 4: Development of MLI2 cells
Some custom functions for Seurat/LIGER object manipulation and analysis (not yet available in LIGER) are included in cb_custom_functions.R and src.
Processed count matrices can be downloaded from GEO and Single Cell Portal. Additional metadata and smFISH
data are available in data. Original individual cell type analysis objects (Seurat/LIGER) can be made available upon request; UMAP and t-SNE coordinates corresponding to many individual analysis objects are available in data.
First round annotations for all recovered nuclei profiles (780,553 + 11,812 FACS sorted putative Purkinje profiles) are available in data/full_cb_metadata.csv.