This repository contains scripts used in our analysis of primate GM effects on mouse brain gene expression.
We ran most analysis steps using R (v4.1). We recommend the following utility or visualization packages to extend base R's functionality.
The following files are expected:
Mouse experiment - brain RNAseq data:
- A .csv file containing count data
data/counts.csv - A .csv file containing metadata data
data/mouse_meta.csv - A .csv file containing technical metadata data
data/mouse_tech_meta.csv - A .csv file containing normalized expression data
data/exp-data-matched-to-pathways.csv
Mouse experiment - GM data:
- A .csv file containing pathway data
data/pathway-data-matched-to-expression.csv
Published datasets:
- An .rds file containing primate expression data (from Zhu et al. 2018)
data/human_v_macaque_zhu_MFC.rds - A .csv file containing the results from Dumas et al. 2021
data/dumas.csv - A .tsv file containing disease risk genes from the DISEASES database
data/human_disease_associations.tsv - A .txt file containing network parameters for MiMeNet analysis
data/network_parameters.txt
- Key libraries: variancePartition, BRETIGEA, biomaRt, ggplot2, corrplot
scripts/mouse-code-final.R
MiMeNet analysis
- Key libraries: MiMeNet_train.py
scripts/microbiome.sh