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
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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

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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