- Pairwise expression correlations
Differential expression analysis
- Proportion
- DEX genes - IE and exons only (limma)
- GO enrichment and REVIGO
Clustering analysis
- Copy from rosehip paper
- Cluster cohesion/separation
- Build dendrograms
Cluster matching
- Marker score - beta equation
- Threshold score to pick marker genes - correlated expression - reciprocal best match
- Cluster annotation with Tasic et al clusters
- Select best markers of paired clusters
Estimating nuclear proportions
- Intronic read ratio
- Top 3 gene expression ratio
- Compare with variances - propagation of error
- Individual gene estimates
- Comparison with Halpern 2015
In situ measurement of nuclear and soma sizes
- Selected cre-lines
- Neurolucida tracing?
- Tracked cortical depth / layer position
Code availability
Acknowledgements
Competing interests
Figures