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

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

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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 reconstru...

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Bibliographic Details
Main Authors: Ryosuke Matsuzawa, Daichi Kawahara, Makoto Kashima, Hiromi Hirata, Haruka Ozaki
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2025-01-01
Series:PLoS ONE
Online Access:https://doi.org/10.1371/journal.pone.0311296
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Summary: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).
ISSN:1932-6203

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