MyND Project
All code is in R and depends on packages from CRAN and/ or Bioconductor.
This includes code and some plots. Exploratory analysis and intermediate processing files are too large for this repository.
Analysis Pages
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PD Monocyte Analysis:
- Monocyte Quality Control
- Variance Partition
- Differential Gene Expression Result Summary
- L-Dopa Correlation
- WGCNA Eigengene approach. Beeswarm plots for the Figures 3A and 3B.
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Microglia dataset 36 PD vs 116 CT:
- Variance Partition. Cannonical correlation and violin plots from Variance Partition.
- Differential expression analysis. The model accounts for PMI and cause of death. Tool = Limma with Duplicate correlation to account for repeated measures.
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AMP-PD Analyses
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Analysis Scripts