ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets.

ABSTRACT: CITE-seq enables paired measurement of surface protein and mRNA expression in single cells using antibodies conjugated to oligonucleotide tags. Due to the high copy number of surface protein molecules, sequencing antibody-derived tags (ADTs) allows for robust protein detection, improving cell-type identification. However, variability in antibody staining leads to batch effects in the ADT expression, obscuring biological variation, reducing interpretability, and obstructing cross-study analyses. Here, we present ADTnorm (https://github.com/yezhengSTAT/ADTnorm), a normalization and integration method designed explicitly for ADT abundance. Benchmarking against 14 existing scaling and normalization methods, we show that ADTnorm accurately aligns populations with negative- and positive-expressi

SUBMITTER: Zheng Y 

PROVIDER: S-EPMC11261982 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature