Companion software code for the review article by Wang M. et al. (Guidelines for Bioinformatics of Single-Cell Sequencing Data Analysis in Alzheimer’s Disease: Review, Recommendation, Implementation and Application. (2022) Molecular Neurodegeneration.)

Correspondence: Prof. Bin Zhang ([email protected] or [email protected])

This Github page contains R scripts for analyzing the ROSMAP snRNA-seq data developed by Mathys et al. (Nature 2019, 570:332-337 PMID: 31042697) so as to provide concrete guidelines for utilizing the recommended pipelines for analyzing scRNA-seq data in AD.

The filtered count matrix for the ROSMAP study can be downloaded at https://www.synapse.org/#!Synapse:syn18681734. See Section B. Quality Control to Clustering for details on the data download.

• Section A: Overview of Single Cell Sequencing Study Design (Power Analysis): Also, please see a detailed review of power analysis for single-cell RNA-seq study design.
• Section B: Quality Control to Clustering
• Section D-E: Feature selection, dimension reduction & clustering analysis
• Section F: Differential Expression Analysis
• Section H: Copy Number Inference
• Section I: eQTL detection
• Section J: scATAC-seq Analysis
• Section K: Gene Network Analysis (MEGENA, BN)
• Section G: Trajectory Analysis
• Section M: Integration snRNA-seq and bulk RNA-seq datasets
• Section O: Spatial Transcriptome Analysis