OmicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data.

ABSTRACT: The unprecedented speed and sensitivity of mass spectrometry (MS) unlocked large-scale applications of proteomics and even enabled proteome profiling of single cells. However, this fast-evolving field is hindered by a lack of scalable dimensionality reduction tools that can compensate for substantial batch effects and missingness across MS runs. Therefore, we present omicsGMF, a fast, scalable, and interpretable matrix factorization method, tailored for bulk and single-cell proteomics data. Unlike current workflows that sequentially apply imputation, batch correction, and principal component analysis, omicsGMF integrates these steps into a unified framework, dramatically enhancing data processing and dimensionality reduction. Additionally, omicsGMF provides robust imputation of missing val

SUBMITTER: Segers A 

PROVIDER: S-EPMC11974731 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature