Recent developments in single-cell analysis has provided the ability to assay >50 surface-level proteins by combining oligo-conjugated antibodies with sequencing technology. These methods, such as CITE-seq and REAP-seq, have added another modality to single-cell analysis, enhancing insight across many biological subdisciplines. While packages like Seurat have greatly facilitated analysis of single-cell protein expression, the practical steps to carry out the analysis with increasingly larger datasets have been fragmented. In addition, using data visualizations, I will highlight some details about the centered log-ratio (CLR) normalization of antibody-derived tag (ADT) counts that may be overlooked. In this method chapter, I provide detailed steps to generate CLR-normalized CITE-seq data using cloud computing from a large CITE-seq dataset.
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