thebiohub/xenium repository overview

⁠10x Genomics Xenium In Situ Analysis Pipeline

A containerized end-to-end workflow for spatial transcriptomics data generated by the 10x Genomics Xenium In Situ platform, enabling reproducible analysis from raw outputs to spatially-resolved biological insights.

⁠Workflow Steps

1. Preprocessing — import Xenium output bundles (cell feature matrix, transcripts, boundaries)
2. Quality Control — cell-level QC filtering by transcript counts, gene detection, and cell area
3. Normalization — log-normalization and feature selection
4. Analysis — clustering, cell type annotation, differential expression, spatially variable gene detection
5. Visualization — spatial feature plots, UMAP embeddings, and publication-ready figures

⁠Usage

docker pull thebiohub/xenium

⁠Requirements

• Docker 20.10+
• Minimum 32GB RAM recommended for large Xenium datasets

⁠Maintained by

TheBioHub⁠