BxGenomics

BxGenomics is a comprehensive, web-based platform designed to give biologists an efficient and user-friendly solution for the analysis, visualization, and data mining of both single-cell and bulk RNA-Seq data. The platform requires no coding experience and is suitable for anyone with a basic interest in RNA-Seq data analysis, from bench scientists to experienced bioinformaticians. BxGenomics combines powerful best-practice analytical pipelines, an extensive repository of preloaded public datasets, and interactive visualization tools capable of generating publication-ready figures.

The platform is built on a strong scientific foundation, with its core components — including scRNASequest, CellDepot, RNASequest, OmicsView, and QuickOmics — published or submitted in peer-reviewed journals such as BMC Genomics, Journal of Molecular Biology, Computational and Structural Biotechnology, and Bioinformatics. BxGenomics takes these open-source solutions and delivers them as a fully supported, ready-to-use system with major enhancements and expert bioinformatics support.

Single-Cell RNA-Seq Analysis and Mining

• The scRNA-Seq analysis pipeline integrates several popular tools including Seurat, Scanpy, Harmony, and LIGER, providing a semi-automated workflow for processing raw data, batch correction using multiple harmonization methods, reference-based cell type label transfer, and multi-sample multi-condition differential gene expression analysis.
• The integrated web database includes scRNA-Seq results from over 1,000 published datasets encompassing more than 17 million cells, as well as each user's private datasets.
• Users can search the database using multiple attributes such as publication, keywords, species, and cell types, and use advanced filters to compare gene expression across datasets.
• Each dataset can be loaded into the cellxgene VIP visualization tool, which supports rapid, interactive, and scalable exploration of scRNA-Seq results including cell composition, gene expression profiles, and differentially expressed genes across cell types.
• Cellxgene VIP provides over 20 commonly used plotting functions, including: multi-tSNE/UMAP plots, dual-gene plots highlighting co-expression, stacked barplots for cell type fractions across samples, trackplots for lineage marker gene expression, violin plots, Sankey/Riverplots for exploring interdependent variable relationships, density plots, stacked violin and dot plots, and a Command Line Interface via a mini Jupyter Notebook for maximal analytical flexibility.
• Private single-cell data are analyzed using BxGenomics' best-practice pipeline, while public datasets are either provided by authors or curated using the same pipeline.

Bulk RNA-Seq Analysis and Mining

• The bulk RNA-Seq pipeline provides highly automated analysis with robust statistical algorithms, supporting input as raw FASTQ files or pre-computed gene count and TPM files.
• The platform includes approximately 700,000 human samples from over 12,000 projects sourced from GEO and SRA, with sample metadata extracted and available for annotating samples and specifying comparison conditions.
• Gene count data is used for statistical analysis and differential gene expression (DEG), while gene TPM data is used for expression visualization.
• The QuickOmics tool, an R Shiny-powered application, enables biologists to fully explore RNA-Seq results through a broad range of secondary and tertiary analytical tasks with customizable options and both interactive and publication-ready plots.
• QuickOmics analytical modules include: PCA for sample relationship analysis, volcano plots for DEG visualization, correlation analysis between comparisons, pattern clustering for identifying gene subsets with similar expression, heatmaps for gene cluster identification, KEGG pathway enrichment analysis with cellular context display, and correlation network analysis for exploring links between genes of interest.
• Differential gene expression analysis is performed using limma or DESeq2, and gene counting is supported via Subread/Featurecount, STAR/RSEM, Kallisto, or Salmon depending on the project.
• Users can perform DEG analysis and pathway enrichment directly from the Bulk RNA View interface without any coding, using a guided setup page to define comparisons of interest.

Data Analysis Service and Workflow

• Users can submit raw data and sample descriptions to receive a professional analysis report and personalized online database within 1–2 weeks.
• The service includes comprehensive QC of raw data and gene counts, robust statistical analysis for DEGs, advanced functional pathway analysis, and expert review of all results before delivery.
• Once data is uploaded to the BxGenomics platform, authorized users can access results via a browser from anywhere with an internet connection at any time.
• Different gene ID types are automatically recognized and converted, enabling seamless integration of gene expression data across projects analyzed with different gene ID formats.
• The platform serves dual purposes: as a data mining system for continuous discovery across all RNA-Seq results in a laboratory, and as a long-term data archive system for data longevity and sustained access.
• The BxGenomics service team consists of highly educated scientists and customer support managers with decades of experience in biological studies and genomics, providing continuous high-quality technical support throughout every project.

BxGenomics is accessible as a web-based platform, requiring no local installation, and supports both private and public datasets. The system is underpinned by peer-reviewed methodologies and integrates established open-source bioinformatics tools into a cohesive, fully supported environment, making it well suited for life sciences research teams seeking scalable, expert-backed RNA-Seq analysis and data mining capabilities.