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Poly Pipeline: A Polyvalent Spatial Transcriptomics Workflow Validated Across Polyploid and Diploid Organisms

Carvalho, P. C.; Millsteed, T.; Henry, R. J.

2026-09-04 bioinformatics
10.64898/2026.08.31.748304 bioRxiv
Show abstract

Spatial transcriptomics (ST) has emerged as a transformative approach for visualizing tissue landscapes, yet it faces significant challenges regarding data standardization, sparsity, and the analysis of complex genomes, particularly polyploid plants. To address these limitations, we introduce Poly Pipeline, a robust and universal bioinformatic workflow designed to streamline analysis across diverse plant and animal genomes. The pipeline integrates a comprehensive converter for proprietary formats, clustering algorithms, and hdWGCNA co-expression networks, which indirectly preserves the expression signatures of low-expressed duplicated genes. Benchmarking across datasets from wheat, rice, Arabidopsis, and mouse demonstrated the broad applicability of the pipeline in identifying relevant clusters, showing effectiveness across diverse organisms and data types. By providing a unified and reproducible framework, Poly Pipeline addresses a critical gap in analyzing genomic redundancy, especially that related to polyploidy, and promotes FAIR data principles for the broader scientific community.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.