thebiohub/geomx repository overview

⁠NanoString GeoMx Digital Spatial Profiling (DSP) Analysis Pipeline

A containerized end-to-end workflow for spatial transcriptomics data generated by the NanoString GeoMx DSP platform, enabling reproducible analysis from raw data to biologically meaningful results.

⁠Workflow Steps

1. Preprocessing — import and parse DCC files and sample annotation sheets
2. Quality Control — segment- and probe-level QC flagging and filtering
3. Normalization — Q3, housekeeping gene, and background normalization
4. Analysis — differential expression, dimensionality reduction (PCA, UMAP)
5. Visualization — spatial heatmaps, violin plots, and publication-ready figures

⁠Key Tools

• GeomxTools / GeoMxWorkflows (Bioconductor)
• ggplot2 for visualization

⁠Usage

docker pull thebiohub/geomx

⁠Requirements

• Docker 20.10+
• Minimum 16GB RAM recommended

⁠Maintained by

TheBioHub⁠