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OmnibusX: A unified platform for accessible multi-omics analysis.

Linh Truong·Thao Truong·Huy Nguyen
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Abstract

OmnibusX is an integrated, privacy-centric platform that enables code-free multi-omics data analysis by bridging computational methodologies with user-friendly interfaces. Designed to overcome challenges posed by fragmented analytical tools and high computational barriers, OmnibusX consolidates workflows for diverse technologies - including bulk RNA-seq, single-cell RNA-seq, single-cell ATAC-seq, and spatial transcriptomics - into a single, cohesive application. The application integrates established open-source tools such as Scanpy, DESeq2, SciPy, and scikit-learn into transparent, reproducible pipelines, offering users control over analytical parameters. Additionally, OmnibusX features proprietary modules, including a highly accurate cell-type prediction engine and an interactive plotting editor for generating publication-quality visualizations. Available as a standalone desktop application and an enterprise edition for centralized server deployment, OmnibusX ensures all data processing is conducted locally, eliminating external data transfer and usage tracking. By lowering technical barriers and enhancing reproducibility, OmnibusX aims to accelerate biological discovery and foster robust, data-driven collaborations. A fully documented trial version is accessible at: https://omnibusx.com/apps.

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Computational BiologySoftwareHumansSingle-Cell AnalysisGenomicsGene Expression ProfilingReproducibility of ResultsMultiomicsJournal Article

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Linh Truong, Thao Truong, Huy Nguyen. 2025-09-08. OmnibusX: A unified platform for accessible multi-omics analysis.. https://doi.org/10.1371/journal.pcbi.1013480

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