SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Spatial barcoding-based transcriptomic (ST) data require deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER tackles platform effects between ST and scRNA-seq data, ensuring a linear relationship between them while addressing sparsity and spatial correlations in cell types across capture spots. SDePER estimates cell-type proportions, enabling enhanced resolution tissue mapping by imputing cell-type compositions and gene expressions at unmeasured locations. Applications to simulated data and four real datasets showed SDePER's superior accuracy and robustness over existing methods.
Authors
- Wenhao Jiang (ORCID: https://orcid.org/0000-0003-1687-8902)
- Xiayuan Huang (ORCID: https://orcid.org/0000-0002-3325-933X)
- Nating Wang
- A. Justet
- Iván O. Rosas (ORCID: https://orcid.org/0000-0003-4622-618X)
- Zuoheng Wang (ORCID: https://orcid.org/0000-0002-7251-3687)
- Ningshan Li (ORCID: https://orcid.org/0000-0003-1916-2563)
- Taylor Adams (ORCID: https://orcid.org/0000-0003-4280-9070)
- Jiayi Zhao (ORCID: https://orcid.org/0000-0002-7271-4796)
- Robert Homer (ORCID: https://orcid.org/0000-0002-2055-5885)
- Amei Amei (ORCID: https://orcid.org/0000-0003-1045-2345)
- Xiting Yan (ORCID: https://orcid.org/0000-0001-8688-9004)
- Naftali Kaminski (ORCID: https://orcid.org/0000-0001-5917-4601)
- Yunqing Liu (ORCID: https://orcid.org/0000-0003-3515-2314)
- Gang Xu (ORCID: https://orcid.org/0000-0002-2805-9034)
- Ji Qi
- Huanhuan Wei (ORCID: https://orcid.org/0000-0002-6481-5407)
Institutions
- Centre National de la Recherche Scientifique (FR)
- University of Nevada, Las Vegas (US)
- Baylor College of Medicine (US)
- Shanghai Jiao Tong University (CN)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Yale University (US)
- Normandie Université (FR)
- Centre Hospitalier Universitaire de Caen Normandie (FR)
- Chinese University of Hong Kong, Shenzhen (CN)
- Yale New Haven Health System (US)
- University of Hong Kong - Shenzhen Hospital (CN)
- Shenzhen Second People's Hospital (CN)
- Imagerie et Stratégies Thérapeutiques pour les Cancers et Tissus cérébraux (FR)
- Université de Caen Normandie (FR)
Publication Details
- Journal
- Genome biology
- Published
- 2024-10-14
- DOI
- https://doi.org/10.1186/s13059-024-03416-2
- Citations
- 6
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 1.40
Funders
- National Science Foundation
- Foundation for the National Institutes of Health
- Philippe Foundation
- National Institutes of Health