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

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Understanding spatial gene expression is crucial for deciphering cellular functions.
• Existing methods often lack the resolution or scope to capture genome-wide 3D expression patterns.

Purpose of the Study:

• To develop and present tomoseqr, an R package for RNA tomography.
• To enable the reconstruction and visualization of 3D spatial gene expression patterns from 1D tomo-seq data.

Main Methods:

• RNA tomography was computationally applied to reconstruct 3D gene expression.
• The tomoseqr R package was developed for analyzing tomo-seq data.
• User-friendly graphical interfaces were integrated for ease of use.

Main Results:

• The tomoseqr package successfully reconstructs genome-wide 3D spatial gene expression patterns.
• Effectiveness was demonstrated using both simulated and real tomo-seq datasets.
• The utility of the package for researchers was validated.

Conclusions:

• tomoseqr provides a robust and accessible tool for RNA tomography analysis.
• The package facilitates the visualization of complex 3D gene expression landscapes.
• tomoseqr is a valuable resource for advancing spatial transcriptomics research.