The monocyte transcriptome predicts microglial activation and amyloid deposition in aging.

This git repo includes all code used for the following analyses:

1. RNAseq gene expression quality control, normalization, and co-variate selection for monocyte and DLPFC bulk brain tissue samples in ROS/MAP
2. Cross-tissue correlation analyses, including functional enrichment and plotting
3. Cis-eQTL analysis of monocyte gene expression
4. Transcriptome-wide differential expression analysis for monocyte and DLPFC datasets, including plotting summary and individual-level results
5. Functional enrichment of differential expression results
6. Full pipeline for Weighted Gene Co-expression Network Analysis (WGCNA) for both monocyte and DLPFC datasets, including visualizations
7. Model building, validation, and final specification for top genes from monocyte differential expression in predicting neuropathology and cognition

Data used for these analyses are available through Synapse under the following accession codes: ....