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bioRxiv · 10.1101/2025.06.11.659031

Cross-Platform Omics Pipeline for Integrated Transcriptomics

Gao, L.·Hao, J.·Xin, Z.·Le, H.
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Abstract

The fragmentation of single-cell RNA-seq (scRNA-seq) and spatial transcriptomics (ST) tools across Python/R ecosystems, coupled with escalating computational demands for million-cell datasets, creates critical barriers to reproducible analysis. To overcome this, we present CrosPIT (Cross-Platform Omics Pipeline for Integrated Transcriptomics), a cloud-native framework that unifies cross-language analysis in Google Colab with versioned storage on Google Drive. Pre-configured environments enable rapid switching between CPU/GPU/R runtimes, eliminating local hardware constraints. To demonstrate biological utility, we embedded several modules, such as a module for precision detection of malignant epithelial cells in colorectal cancer. CrosPIT thus delivers a scalable, language-agnostic solution that standardizes workflows through native AnnData/Seurat object interoperability, accelerates integrative omics research, and democratizes access to high-performance transcriptomic analysis.

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Gao, L., Hao, J., Xin, Z., Le, H.. 2025-06-12. Cross-Platform Omics Pipeline for Integrated Transcriptomics. https://doi.org/10.1101/2025.06.11.659031

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