Evidence map›Paper›PMID 39774435›Full record

ArticlePloS one2025

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

Abstract read
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In one paragraph

Article in PloS one, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Ryosuke MatsuzawaMaster's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.ORCID 0000-0003-2999-4734
Daichi KawaharaDepartment of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Kanagawa Japan.
Makoto KashimaDepartment of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Kanagawa Japan.
Hiromi HirataDepartment of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Kanagawa Japan.
Haruka OzakiBioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.ORCID 0000-0002-1606-2762

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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).

Indexed as

Imaging, Three-DimensionalSoftwareAnimalsGene Expression ProfilingHumansRNASequence Analysis, RNATomographyRNA

Identifiers

PMID39774435
PMCPMC11709299

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.