This repo contains the code used to develop the manuscript "Discovering stimulatory state specific type 2 diabetes GWAS mechanisms with single-cell multi-omics on iPSC-derived fibro-adipogenic progenitors."
FUSION analyses (figure 1 and supp fig 1):
- FAP abundance analyses
- Milo analyses
- Testing for significantly different peak
Differentiation analyses (figure 2 and supp fig 2):
- Line plot of differentiation
- Bulk RNA-seq analysis
- Jaccard similarity score
- Logistic regression to FUSION
Insulin stimulated glucose uptake assay analyses (figure 3 and supp fig 3):
- Census-seq analyses and roll call heatmap
- Histogram of differentiations/R analysis of differentiations
- Luminesence analyses/LMM analyses of luminesence
FAP Cell Village Multiome analyses (figure 4, supp fig 4, and supp table 1-3):
- Census-seq analysis
- Initial RNA/ATAC analyses
- Multiome QC/doublet detection
- Setting up UCSC browser
- RNA clustering
- Spearman correlation to FUSION
- Differential gene expression (MAST, clusterProfiler)
- Differential peak identification
- Transcription factor motif enrichment
FAP sub-types (figure 5 and supp fig 5):
- Pseudotime analyses
- Milo analyses
- Binomial test
- Setting up UCSC by sub-type
- GWAS enrichment analyses
- SCENT analyses