{"repo":"yezhengSTAT/ADTnorm","free":true,"listed":false,"github":"https://github.com/yezhengSTAT/ADTnorm","clone":"git clone https://github.com/yezhengSTAT/ADTnorm.git","description":"ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.","language":"R","stars":31,"topics":["single-cell","cite-seq","data-integration","surface-protein-normalization"],"license":"GPL-3.0","category":"data-pipelines","readme_excerpt":"ADTnorm What is ADTnorm ? 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, 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-expression of surface protein markers across 13 public datasets, effectively removing technical variation across batches and improving cell-type separation. ADTnorm enables efficient integration of public CITE-seq datasets, each with unique experimental designs, paving the way for atlas-level analyses. Beyond normalization, ADTnorm aids in automated threshold-gating as well as assessment of antibody staining quality for titration optimization and antibody panel selection. This repository is the ADTnorm R package. We also provide a Python wrapper by Daniel P. Caron. Manuscript: Zheng et al. ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets. Nature Communications. 2025 ADT Norma","default_branch":null,"files":null,"tree":[],"storefront":"/r/yezhengSTAT","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/yezhengSTAT/ADTnorm/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}