CyTOF_scRNA_integration

This repository contains the code for our study for the integration of CyTOF and scRNA-seq datasets:

Repapi et al. (2022) Integration of single-cell RNA-Seq and CyTOF data characterises heterogeneity of rare cell subpopulations

This repository contains a record of the code we used for the analyses in this paper. To run the same analyses you will need the same versions of software and packages as we used (see below). However, we can not guarantee that it will execute properly or generate the same results with new versions of any of the software.

R package versions

The following R packages were used for the data analysis of our paper:

scuttle_1.4.0
flipPlots_1.3.5
mclust_5.4.9                
ggrepel_0.9.1               
patchwork_1.1.1            
GGally_2.1.2                
Matrix_1.4-0                
tidyr_1.2.0                 
cowplot_1.1.1               
ggplot2_3.3.5              
dplyr_1.0.8                 
SeuratObject_4.0.4          
Seurat_4.1.0                
SingleCellExperiment_1.16.0 
SummarizedExperiment_1.24.0
Biobase_2.54.0              
GenomicRanges_1.46.1        
GenomeInfoDb_1.30.1         
IRanges_2.28.0              
S4Vectors_0.32.3           
BiocGenerics_0.40.0         
MatrixGenerics_1.6.0        
matrixStats_0.61.0
reshape2_1.4.4              
RColorBrewer_1.1-2          
ComplexHeatmap_2.10.0       
circlize_0.4.14             
CATALYST_1.18.1
htmlwidgets_1.5.4