This directory contains analysis scripts for comparative snATAC-seq and snRNA-seq experiments performed on human, chimpanzee and rhesus macaque.
The folders are organized as:
snATAC_seq: Scripts to preprocess snATAC-seq dataset after peak calling. Scripts are numbered based on their order.
01: Finds consensus peaks (aka CREs) across samples per species.
02: Finds common CREs across species (uses liftOver on chimpanzee and macaque to find common coordinates with human).
03: Finds overlap between raw reads and final set of CREs in each species own coordinates.
04: Generates CRE-Cell count matrix.
05: Dimensionality reduction and cell clustering per species.
06: Gene activity scores per cell using Cicero.
07: Broad annotation of cell types per species.
08: Subtype annotation of broadly annotated cell types per species. Accompanying snRNA-seq is used as a reference to achieve this.
09: Differentially accessible region analysis between species per cell type.
10: Motif enrichments of CREs with human-specific accessibility per cell type.
11_01: Human accelerated region (HAR) identification on cortical CREs.
11_02_03: Human accelerated region (HAR) enrichments of differentially accessible CREs between species.
12_01: Identify modern human-specific substitutions by comparing to 3 neanderthals and 1 denisovan.
12_02: Enrichment between modern human-specific substitutions and human-specific CRE accessibility changes per cell type.
13: Overlap of differentially accessible CREs and DEGs per species per cell type compared to randomized background.
14: Identification of human-specific substitutions within CREs compared to great ape species.
snRNA_seq: Scripts to preprocess snRNA-seq dataset after count matrix generation. Scripts are numbered based on their order.
01: Broad annotation of cell types per species.
02: Subtype annotation of broadly annotated cell types after integrating species to identify homologous cell types.
03: Statistical comparison of cell type ratios between species.
04: Differential gene expression (DEG) analysis between species and identification of species-specifically regulated genes.
05: Gene ontology (GO) enrichment of DEGs between species.
Supplementary_Functions: Contains functions used in other scripts
Please do not hesitate contact me with any questions: emre.caglayan@utsouthwestern.edu