Data and code associated with the integrated analysis (Figure 4) in paper:
Developmental diversification of cortical inhibitory interneurons
by Christian Mayer#, Christoph Hafemeister#, Rachel C. Bandler#, Robert Machold, Renata Batista Brito, Xavier Jaglin, Kathryn Allaway, Andrew Butler, Gord Fishell* and Rahul Satija*
# Equal contribution * Corresponding authors
Published in Nature (2018), DOI 10.1038/nature25999
Preprint on bioRxiv (2017), DOI 10.1101/105312
The examples subfolder contains an commented R Markdown file (and compiled HTML) for the integration of E18 and P56 datasets.
The R subfolder contains code used to generate Figure 4 and components of Extended Data Figures 5-10.
There are individual scripts for the different parts of the analysis. Run them in this order:
- Rscript R/1_integrated_analysis.R
- Rscript R/2_cell-assignment.R
- Rscript R/3_conserved_marker_genes.R
- Rscript R/4_subtype_analysis.R
- Rscript R/5_tsne_mappings.R