Repository for analyses performed in "NeMO Analytics: A 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/

This directory contains the R scripts used to reproduce the core analyses in the manuscript.

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

R code used for performing gene set enrichment analysis: GSEAcode_SonthaliaEtAl.R

R 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: GeneCart2idCols.R

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

This directory contains the data files used in the manuscript.

Gene loadings from the 3 decompositions in the paper: SonthaliaEtAl_SupplTable1_p7CtxDev_GeneLoadings.txt; SonthaliaEtAl_SupplTable2_p40CtxDev_GeneLoadings.txt; SonthaliaEtAl_SupplTable3_p20CtxLayers_GeneLoadings.txt

Gene lists used in the GSEA were obtained from: https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2023.1.Hs/ and CtxDiseaseGeneListsPLUS.RData from PMID: 40634286

This directory contains tools that prepare expression matrices, metadata tables, and h5ad files for upload to NeMO Analytics. The tools fall into two complementary modules:

• exprs_NeMO: R-based utilities for exporting processed matrices and metadata into NeMO-compatible upload packages.
• h5ad_NeMO: Python-based utilities for transforming .h5ad files into NeMO upload formats. Each module includes its own dedicated documentation (.md), which provides input requirements, parameter descriptions, example commands, and output structure.

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:

• Uploading datasets to NeMO: https://nemoanalytics.org/upload_dataset.html
• Dataset Explorer: https://nemoanalytics.org/dataset_explorer.html
• Gene List Manager: https://nemoanalytics.org/gene_list_manager.html

For more general info on dataset collections and computational tools go to: https://www.carlocolantuoni.org/