Multimodal hierarchical classification of CITE-seq data

We describe MultiModal Classifier Hierarchy (MMoCHi), a marker-based approach for the classification of CITE-seq data, reconciling gene and protein expression without reliance on reference atlases. We benchmark MMoCHi using sorted T lymphocyte subsets and annotate a cross-tissue human immune cell dataset. MMoCHi outperforms leading transcriptome-based classifiers and multimodal unsupervised clustering in its ability to identify immune cell subsets that are not readily resolved and to reveal novel subset markers.