KD-MISC_single-cell-meta-analysis
Analysis scripts for the manuscript "Single-cell Meta-analysis Of Neutrophil Activation in Kawasaki Disease and Multi-system Inflammatory Syndrome in Children"
NOTE: No novel code/scripts are generated from our analysis. All codes used are adopted from the corresponding packages' public tutorials/vignettes used.
Folder Structure
1. Processing, Integration, Annotation, Re-Clustering
Analysis and plotting scripts used for pre-processing all scRNA-seq data until re-clustering
2. Differential Expression & SNEP Identification
Analysis and plotting scripts for differential expression analysis and SNEP identification
3. Single-cell hdWGCNA
Analysis and plotting scripts for single-cell high-dimensional weighted gene co-expression network analysis
4. Target-Pathway Correlation Analysis
Analysis and plotting scripts for correlation analyses
5. Differential Abundance Testing
Analysis and plotting scripts for testing the differential abundance of cell types and neutrophil subpopulations
6. Validation - MIS-C bulk RNA-seq
Analysis and plotting scripts for the validation study (bulk RNA-seq) for independent MIS-C data
7. Validation - KD scRNA-seq
Analysis and plotting scripts for the validation study (single-cell RNA-seq) for independent KD data
8. Visualization Plots
Analysis and plotting scripts for other statistical testing and visualizations including violin, pie chart, bar, box, scatter plots