Tomoseqr：一个用于基于RNA断层扫描进行3D基因表达模式的空间重建和可视化的Bioconductor软件包。
tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography.
作者信息
Matsuzawa Ryosuke, Kawahara Daichi, Kashima Makoto, Hirata Hiromi, Ozaki Haruka
机构信息
Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.
出版信息
PLoS One. 2025 Jan 8;20(1):e0311296. doi: 10.1371/journal.pone.0311296. eCollection 2025.
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).
RNA断层扫描通过对沿三个正交轴的冷冻切片样本进行RNA测序所生成的一维断层测序数据，在全基因组范围内以计算方式重建三维空间基因表达模式。我们开发了tomoseqr，这是一个用于对断层测序数据进行RNA断层扫描分析的R包，通过用户友好的图形界面来重建和可视化三维基因表达模式。我们使用模拟和真实的断层测序数据展示了tomoseqr的有效性，验证了其对研究人员的实用性。R包tomoseqr可在Bioconductor（https://doi.org/doi:10.18129/B9.bioc.tomoseqr）和GitHub（https://github.com/bioinfo-tsukuba/tomoseqr）上获取。
Zotero 插件