Feiyang Huang

Machine Learning @ Weill Cornell Medicine



Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data


Journal article


Brendan F Miller, Feiyang Huang, Lyla Atta, Arpan Sahoo, Jean Fan
Nature communications, vol. 13, Nature Publishing Group, 2022, pp. 1--13

Link to paper
Cite

Cite

APA   Click to copy
Miller, B. F., Huang, F., Atta, L., Sahoo, A., & Fan, J. (2022). Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data. Nature Communications, 13, 1–13.


Chicago/Turabian   Click to copy
Miller, Brendan F, Feiyang Huang, Lyla Atta, Arpan Sahoo, and Jean Fan. “Reference-Free Cell Type Deconvolution of Multi-Cellular Pixel-Resolution Spatially Resolved Transcriptomics Data.” Nature communications 13 (2022): 1–13.


MLA   Click to copy
Miller, Brendan F., et al. “Reference-Free Cell Type Deconvolution of Multi-Cellular Pixel-Resolution Spatially Resolved Transcriptomics Data.” Nature Communications, vol. 13, Nature Publishing Group, 2022, pp. 1–13.


BibTeX   Click to copy

@article{miller2022a,
  title = {Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data},
  year = {2022},
  journal = {Nature communications},
  pages = {1--13},
  publisher = {Nature Publishing Group},
  volume = {13},
  author = {Miller, Brendan F and Huang, Feiyang and Atta, Lyla and Sahoo, Arpan and Fan, Jean}
}

Recent technological advancements have enabled spatially resolved transcriptomic profiling but at multi-cellular pixel resolution, thereby hindering the identification of cell-type-specific spatial patterns and gene expression variation. To address this challenge, we develop STdeconvolve as a reference-free approach to deconvolve underlying cell types comprising such multi-cellular pixel resolution spatial transcriptomics (ST) datasets. Using simulated as well as real ST datasets from diverse spatial transcriptomics technologies comprising a variety of spatial resolutions such as Spatial Transcriptomics, 10X Visium, DBiT-seq, and Slide-seq, we show that STdeconvolve can effectively recover cell-type transcriptional profiles and their proportional representation within pixels without reliance on external single-cell transcriptomics references. STdeconvolve provides comparable performance to existing reference-based methods when suitable single-cell references are available, as well as potentially superior performance when suitable single-cell references are not available. STdeconvolve is available as an open-source R software package with the source code available at https://github.com/JEFworks-Lab/STdeconvolve.

Share




Follow this website


You need to create an Owlstown account to follow this website.


Sign up

Already an Owlstown member?

Log in