/Mayer-et-al-2018_IntegratedAnalysis

Data and code associated with the integrated analysis (Figure 4) in Mayer et al 2018

Primary LanguageRGNU General Public License v3.0GPL-3.0

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.

How to run

There are individual scripts for the different parts of the analysis. Run them in this order:

  1. Rscript R/1_integrated_analysis.R
  2. Rscript R/2_cell-assignment.R
  3. Rscript R/3_conserved_marker_genes.R
  4. Rscript R/4_subtype_analysis.R
  5. Rscript R/5_tsne_mappings.R