Data and code for Fitzgerald et al: MDD seeded co-expression networks

Below is a decription of the data and code supplied within this repository related to Fitzgerald et al "Astrocyte fatty acid metabolism as a driver of risk for major depressive disorder" Generated data Data About All_GTEx_DLPFC_networks.RData Non-thresholded coexpression summary statistics for MDD risk genes in GTEx frontal cortex my_big_negative_GTEx_DLPFC_list.RData "All_GTEx_DLPFC_networks.Rdata" data filtered to those genes with R < -0.5 and FDR < 0.05 my_big_positive_GTEx_DLPFC_list.RData "All_GTEx_DLPFC_networks.Rdata" data filtered to those genes with R > 0.5 and FDR < 0.05 Generated code File About Related figure Chang_bootstrap.R Bootstrapping of coexpression networks in the Chang et all data for comparing FADS1 coexpressed genes across disease states Fig 4G CMC_QC.R Quality control for the common mind consortium data for validation of coexpression networks Supp Cont_vs_MDD_modscores.R Generating module scores in snRNA-seq data Fig 4E FADS1_clustering.R Clustering of snRNA-seq data using genes coexpressed with FADS1 Fig 5 gene_analysis.sh Annotation of GWAS summary statistics using Hi-C data Fig 2A gene_set_analysis.sh GWAS enrichment analysis using MAGMA Fig 6C GTEx_coexp_networks.R Generating seeded coexpression networks for MDD risk genes in the GTEx dataset Fig 2B GTEx_QC_1.R Filtering of the GTEx dataset NA GTEx_QC_2.R Normalisation and regression of technical covariates from the GTEx data NA Labonte_et_al_QC.R Quality control, filtering and regression of technical covariates from the Labonte et al dataset Fig 4F Milo_analysis.R Neighbourhood based analysis for differentially abundant nuclei between control and MDD nuclei Fig 5H Nagy_et_al_astro_subsetting.R Subsetting astrocytes from the full Nagy et al snRNA-seq dataset NA Network_analysis.R To generate and analyse a graph of coexpression networks Fig 3E NicheNet.R For a NicheNet analysis to infer patterns of cell-cell communication Fig 6F Vizium_analysis.R Processing spatial RNA-seq data and generating cell scores for spatial inference of identified cell states Fig 5F