FAP_paper

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):

1. FAP abundance analyses
2. Milo analyses
3. Testing for significantly different peak

Differentiation analyses (figure 2 and supp fig 2):

1. Line plot of differentiation
2. Jaccard similarity score
3. Logistic regression to FUSION

Insulin stimulated glucose uptake assay analyses (figure 3 and supp fig 3):

1. Census-seq analyses and roll call heatmap
2. Histogram of differentiations/R analysis of differentiations
3. Luminesence analyses/LMM analyses of luminesence

FAP Cell Village Multiome analyses (figure 4, supp fig 4, and supp table 1-3):

1. Census-seq analysis
2. Initial RNA/ATAC analyses
3. Multiome QC/doublet detection
4. Setting up UCSC browser
5. RNA clustering
6. Spearman correlation to FUSION
7. Differential gene expression (MAST, clusterProfiler)
8. Differential peak identification
9. Transcription factor motif enrichment

FAP sub-types (figure 5 and supp fig 5):

1. Pseudotime analyses
2. Milo analyses
3. Binomial test
4. Setting up UCSC by sub-type
5. GWAS enrichment analyses
6. SCENT analyses