CAMML with the Integration of Marker Proteins (ChIMP)

Abstract

MotivationCell typing is a critical task in the analysis of single cell data, particularly when studying diseased tissues that contain a complex mixture of normal tissue and infiltrating immune cells. Unfortunately, the sparsity and noise of single cell data make accurate cell typing at the level of individual cells extremely difficult. To address these challenges, we previously developed the CAMML method for multi-label cell typing of single cell RNA-sequencing (scRNA-seq) data. CAMML uses weighted gene sets to score each profiled cell for multiple potential cell types. While CAMML outperforms other scRNA-seq cell typing techniques, it only leverages transcriptomic data so cannot take advantage of newer multi-omic single cell assays that jointly profile gene expression and protein abundance (e.g., joint scRNA-seq/CITE-seq). ResultWe developed the ChIMP (CAMML with the Integration of Marker Proteins) method to support multi-label cell typing of individual cells jointly profiled via scRNA-seq and CITE-seq. ChIMP combines cell type scores computed on scRNA-seq data via the CAMML approach with discretized CITE-seq measurements for cell type marker proteins. The multi-omic cell type scores generated by ChIMP allow researchers to more precisely and conservatively cell type joint scRNA-seq/CITE-seq data.