NeuronalSwitch

Computational scripts for the paper: Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus

Install

    devtools::install_github("chernolabs/NeuronalSwitch")

Note: the following R packages should also be installed in your system:

SingleCellExperiment, BiocParallel, scater, scran, robustbase, batchelor, slingshot,Seurat,igraph, ggplot, patchwork,dendsort,pheatmap,ComplexHeatmap

Get raw data from GEO

In order to run this computational pipeline you should:

• download into the data_raw folder the 01_DS1x_raw_ssce.Rdata.gz and 02_DS2_raw_ssce.Rdata.gz supplementary files from GEO GSE249794.
• unzip both files using gzip

Pipeline

Directory structure

• data_raw : initial raw data (you should put the count matrices downloaded from GEO here)
• data_aux : some pre-calculated intermediate files provided to alleviate processing time (including 04_colDataDS1.Rdata and 05_colDataDS2.Rdata files with clusP and clusP2 cluster labels for the final datasets)
• data : working directory
• data_figs: output figures

You should sequentially apply the following R scripts.

script
01_sce_DS1x.R	Preprocessing and QC of DS1 raw data
02_sce_DS2.R	Preprocessing and QC of DS2 raw data
03_DS1x_DS2_comparison.R	Data integration, replicability analysis
04_sce_DS1.R	De-novo reprocessing and QC of dataset1
05_DS2_labelTransfer.R	Seurat cluster label's transfer
06_DS1_MKNN_fig.R	MKNN graph cluster and density figures
07_DS1_pseudotemp.R	Pseudotime estimation for DS1
07_DS2_pseudotemp.R	Pseudotime estimation for DS2
08_density_pseudot.R	Pseudotime density plots
09_cascades_TFs.R	Heatmap of TF expression profiles
10_scenic.R	Regulon analysis for DS2