AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics. Issue 4 (10th October 2022)

• Record Type: Journal Article
• Authors: Lund, Jesper B; Lindberg, Eric L; Maatz, Henrike; Pottbaecker, Fabian; Hübner, Norbert; Lippert, Christoph
• Is Part Of: NAR genomics and bioinformatics. Volume 4:Issue 4(2022)
• Publication Date: 2022-10-10
• Subjects: Genomics -- Periodicals; Bioinformatics -- Periodicals; 572.8
• DOI: 10.1093/nargab/lqac073
• Languages: English
• ISSNs: 2631-9268

Abstract

Abstract: With the current surge of spatial transcriptomics (ST) studies, researchers are exploring the deep interactive cell-play directly in tissues, in situ. However, with the current technologies, measurements consist of mRNA transcript profiles of mixed origin. Recently, applications have been proposed to tackle the deconvolution process, to gain knowledge about which cell types (SC) are found within. This is usually done by incorporating metrics from single-cell (SC) RNA, from similar tissues. Yet, most existing tools are cumbersome, and we found them hard to integrate and properly utilize. Therefore, we present AntiSplodge, a simple feed-forward neural-network-based pipeline designed to effective deconvolute ST profiles by utilizing synthetic ST profiles derived from real-life SC datasets. AntiSplodge is designed to be easy, fast and intuitive while still being lightweight. To demonstrate AntiSplodge, we deconvolute the human heart and verify correctness across time points. We further deconvolute the mouse brain, where spot patterns correctly follow that of the underlying tissue. In particular, for the hippocampus from where the cells originate. Furthermore, AntiSplodge demonstrates top of the line performance when compared to current state-of-the-art tools. Software availability: https://github.com/HealthML/AntiSplodge/ .