Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue

Contains all code and data for Werner and Gillis, Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue, 2024. 

Additionally, the code and data for this paper can be found at https://github.com/JonathanMWerner/meta_organoid_analysis with an easy to view github markdown file containing all the code used to generate all figure panel plots at https://github.com/JonathanMWerner/meta_organoid_analysis/blob/main/figure_plots_with_data_code.md.

Due to file size limits on github, there are several data files not available on github, but are available here on zenodo in the data_for_plots.zip file, see below:

umap_embeddings_Fig2A.Rdata
cross_dataset_aggregated_exp_metaMarker_all_fetal_SuppFig1B_Fig2E.Rdata
organoid_egad_results_ranked_6_26_24_Fig3D.Rdata
fetal_egad_results_ranked_6_26_24_Fig3D.Rdata
org_eigenvec_matrices_SuppFig3CD.Rdata

The R package developed for this paper is available at https://github.com/JonathanMWerner/preservedCoexp