Project Overview - snMultiome

This repository contains scripts for the snMultiome postnatal project, focused on the analysis and integration of multi-modal single-cell data, specifically RNA-seq and ATAC-seq. Below is an overview of the scripts used in the project. Further information, including relevant input data files, can be found in synapse under SynID: syn62738189.

SnMultiome Analysis - Preprocessing

• Date: August 2024
• Script Name: preprocess_merge.R
• Description: Pre-processes single-cell RNA-seq and ATAC-seq data from multiple samples using Seurat and Signac, merges data into a single Seurat object, and saves the output.

SnMultiome Analysis - Filtering and Clustering

• Date: August 2024
• Script Name: filter_cluster.R
• Description: Loads a pre-processed Seurat object with multi-modal data (RNA and ATAC-seq), performs filtering, normalization, dimensional reduction, and clustering, then saves the processed object.
• Outputs: Potential plots for Fig. 1b, e.

Variance Partition and crumblr Analysis

• Date: August 2024
• Script Name: VarPart_crumblr.R
• Description: Performs VariancePartition analysis and crumblr.
• Outputs: Potential plots for Fig. 1e, Fig. 5b.

MAGMA and LDsc Analysis

• Date: August 2024
• Script Name: magma_ldsc.R
• Description: Analyzes enrichment (MAGMA / LDsc) and TOBIAS results.
• Outputs: Plots for Fig. 2c, 2e, 3a, 6c, and S6.

HiC - Preprocessing

• Date: August 2024
• Script Name: HiC_abc.sh
• Description: Pre-processes Hi-C for input in ABC analysis.

ABC-Max Analysis

• Date: August 2024
• Script Name: abcmax.R
• Description: Processes genomic data for various GWAS traits and linkage disequilibrium (LD) buddies, focusing on ABC-MAX analysis (peak overlap with GWAS SNPs and causal genes).
• Outputs: Plots for Fig. 3-4, Fig. S8-S17, Table S8-S10.

Pseudotime analysis using Monocle3

• Date: August 2024
• Script Name: pseudotime.R
• Description: Processes a Seurat object, converts it to a Monocle3 cell_data_set, performs trajectory inference, and identifies temporal genes using Moran's I test.
• Outputs: Potential plots for Fig. 5a, c-d.

Hotspot assignment and SCENIC+ correlation with pseudotime

• Date: August 2024
• Script Name: OPCOligo_Hotspot_SCENIC.R
• Description: Performs module scoring and downstream analysis for Hotspot results and pseudotime, including correlation analysis between pseudotime and SCENIC results.
• Outputs: Potential plots for Fig. 5e-f, Fig. 6 a-c.