ArticleBioinformatics (Oxford, England)2026
ASTRO: Automated Spatial-Transcriptome whole RNA Output.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Spatial Glyco-Codes Define Human Liver Pathology and Progression.bioRxiv : the preprint server for biology · 2026Article
- Poly pipeline: a polyvalent spatial transcriptomics workflow validated across polyploid and diploid organisms.GigaByte (Hong Kong, China) · 2026Article
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Authors and funding
9 authors.
Funding
Abstract
motivationDespite significant advances in spatial transcriptomics, the analysis of formalin-fixed paraffin-embedded (FFPE) tissues, which constitute most clinically available samples, remains challenging. Additionally, capturing both coding and non-coding RNAs in a spatial context poses significant challenges. We recently introduced Patho-DBiT, a technology designed to address these unmet needs. However, the marked differences between Patho-DBiT and existing spatial transcriptomics protocols necessitate specialized computational tools for comprehensive whole-transcriptome analysis in FFPE samples.
resultsHere, we present ASTRO, an automated pipeline developed to process spatial transcriptomics data. In addition to supporting standard datasets, ASTRO is optimized for whole-transcriptome analyses of FFPE samples, enabling the detection of various RNA species, including non-coding RNAs such as miRNAs. To compensate for the reduced RNA quality in FFPE tissues, ASTRO incorporates a specialized filtering step and optimizes spatial barcode calling, increasing the mapping rate. These optimizations allow ASTRO to spatially quantify coding and non-coding RNA species in the entire transcriptome and achieve robust performance in FFPE samples. AVAILABILITY AND IMPLEMENTATION: Codes are available at GitHub (https://github.com/gersteinlab/ASTRO) and Zenodo (doi: 10.5281/zenodo.17913760).
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Registered trials
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 Socratic graph.