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CAIMI-WEIGroup / NMH2024_SCZ_DEG_MRI

This repository contains scripts that were used to generate results in Cui et al., (2024).
MIT License
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NMH2024_SCZ_DEG_MRI

This repository contains scripts and data used in Cui et al., (2024).

Data

Scripts

To perform DESeq2 analysis on differential gene expression in SCZ, use R script:

DESeq2analysis.R

To perform DESeq2 analysis on differential transcript expression in SCZ, use R script:

DESeq2isoform.R

To perform gene-set enrichment analysis, use MATLAB scripts:

scripts_enrichment.m

To perform MAGMA gene property analysis, use BASH scripts:

magma_gene_property.sh

To perform PLS correlation analysis between gene expression and GMV, use MATLAB scripts:

scripts_assoc_morph.m

To perform PLS correlation analysis between gene expression, GMV, and connectivity, use MATLAB scripts:

scripts_assoc_edge_FC_PLS.m
scripts_assoc_edge_SC_PLS.m

To perform PLS correlation analysis between gene expression, GMV, and cognitions, use MATLAB scripts:

scripts_assoc_clinical.m