Repository for analyses performed in "A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development" (https://doi.org/10.1101/2024.02.26.581612).

10min video summary of our manuscript: https://youtu.be/IE3itucbig4

Interactive, public data exploration resources can be found at: https://nemoanalytics.org/landing/neocortex/

Data aquisition from NeMO Anlaytics and Joint decomposition performed for analysis in Figures 1, 2 & 3: SJDcode_Figure1n2n3.R

Data aquisition from NeMO Anlaytics and Joint decomposition performed for analysis in Figures 4, 5, & 6: SJDcode_Figure4n5n6.R

GeneCart2idCols.R is a function used in the SJD code (SJDcode_Figure1n2n3.R & SJDcode_Figure4n5n6.R) to create files for the import of joint decomposition results into NeMO Analytics as gene lists for projection.

Conda environment and associated packages used in the pesudotime analysis can be recreated using the Seurat5_R4_3_0.yml file (https://github.com/carlocolantuoni/NeocortexDevelopment_Sonthalia2024/blob/main/Seurat5_R4_3_0.yml) and the command "conda env create -f Seurat5_R4_3_0.yml".

Installation instructions and code for joint matrix decomposition using the SJD package (https://www.biorxiv.org/content/10.1101/2022.11.07.515489v1) can be found here: https://github.com/CHuanSite/SJD

Installation instructions and code for projection analysis using projectR (https://academic.oup.com/bioinformatics/article/36/11/3592/5804979) can be found here: https://www.bioconductor.org/packages/release/bioc/html/projectR.html

youtube playlist for NeMO Analytics tutorials: https://www.youtube.com/playlist?list=PLbeFhDgIkXxe0G1hzEB_vLSP-5qqesNQj

Additional help can be found on the github site for gEAR, the platform on which NeMO Analytics is built (https://github.com/IGS/gEAR/wiki) and on NeMO Analytics webisite itself: https://nemoanalytics.org/upload_dataset.html; https://nemoanalytics.org/dataset_explorer.html; & https://nemoanalytics.org/gene_list_manager.html