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

Ryosuke Matsuzawa^1,2, Daichi Kawahara³, Makoto Kashima^3,4

¹Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.

|January 8, 2025

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).

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