These are the codes used for analysis and figure generation in the manuscript "Transcriptional and Spatial Resolution of Cell Types in the Mammalian Habenula" (Hashikawa, Hashikawa et al. 2020) from the Stuber lab.
The majority of code is based on Seurat v3 package from Satija lab. Detail tutorial can also be found in their website https://satijalab.org/seurat/.
Regulatory analysis is based on SCENIC package from Aerts lab https://github.com/aertslab/SCENIC.
The analysis starts from the "Doublet Detection" code with the data deposited at GEO :GSE 137478. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137478
Deposited data is gene-count matrix data which was generated by processing the FASTQ files through cellranger pipeline for alignment.