CITE-seq is a method for cellular indexing of transcriptomes and epitopes by sequencing. CITE-seq datasets comprise transcriptome-wide measurements for single cells (gene expression) as well as surface protein level information, typically for a few dozens of proteins. The method is described in Stoeckius et al., 2017 and also on the cite-seq.com website.
These notebooks cover different CITE-seq datasets:
analysis of 5k peripheral blood mononuclear cells (PBMCs) showcasing dsb normalisation and data integration with MOFA+ (data by 10x Genomics can be found here).
calculating weighted nearest neighbours for the 5k PBMCs dataset that also demonstrates how to handle multiple multimodal embeddings.