.Rapp.history

Data and code associated with the integrated analysis (Figure 4) in paper: #
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*Developmental diversification of cortical inhibitory interneurons*#
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by Christian Mayer#, Christoph Hafemeister#, Rachel C. Bandler#, Robert Machold, Renata Batista Brito, Xavier Jaglin, Kathryn Allaway, Andrew Butler, Gord Fishell\* and Rahul Satija\*#
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\# Equal contribution  #
\* Corresponding authors#
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Manuscript in Nature, doi:10.1038/nature25999#
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Preprint on [bioRxiv](https://www.biorxiv.org/content/early/2017/09/13/105312)#
doi: [https://doi.org/10.1101/105312](https://doi.org/10.1101/105312)#
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The examples subfolder contains an commented R Markdown file (and compiled HTML) for the integration of E18 and P56 datasets.#
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The R subfolder contains code used to generate Figure 4 and components of Extended Data Figures 5-10.#
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### How to run#
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There are individual scripts for the different parts of the analysis. Run them in this order:#
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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