tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography

Ryosuke Matsuzawa; Daichi Kawahara; Makoto Kashima; Hiromi Hirata; Haruka Ozaki

doi:10.1371/journal.pone.0311296

tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography

PLoS One. 2025 Jan 8;20(1):e0311296. doi: 10.1371/journal.pone.0311296. eCollection 2025.

Authors

Ryosuke Matsuzawa^{1

2}, Daichi Kawahara³, Makoto Kashima^{3

4}, Hiromi Hirata³, Haruka Ozaki²

Affiliations

¹ Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
² Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.
³ Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Kanagawa Japan.
⁴ Department of Biomolecular Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan.

Abstract

RNA tomography computationally reconstructs 3D spatial gene expression patterns genome-widely from 1D tomo-seq data, generated by RNA sequencing of cryosection samples along three orthogonal axes. We developed tomoseqr, an R package designed for RNA tomography analysis of tomo-seq data, to reconstruct and visualize 3D gene expression patterns through user-friendly graphical interfaces. We show the effectiveness of tomoseqr using simulated and real tomo-seq data, validating its utility for researchers. R package tomoseqr is available on Bioconductor (https://doi.org/doi:10.18129/B9.bioc.tomoseqr) and GitHub (https://github.com/bioinfo-tsukuba/tomoseqr).

Copyright: © 2025 Matsuzawa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

MeSH terms

Animals
Gene Expression Profiling / methods
Humans
Imaging, Three-Dimensional* / methods
RNA / genetics
Sequence Analysis, RNA / methods
Software*
Tomography / methods

Substances

RNA

Grants and funding

This work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Number JP 22K15127 to MK, 22K17992 to HO, and JST-Mirai Program Grant Number JPMJMI20G7 to HO. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.