spatialGE (web application)

spatialGE analyzes spatial transcriptomic (ST) data to identify spatial gene expression patterns, detect tissue domains, infer cell-type phenotypes, and compare spatial features across samples.

Key Features:

• Quality control: Provides quality control procedures for spatial transcriptomic data.
• Normalization: Implements normalization procedures for expression matrices.
• Domain detection: Detects spatial domains within tissue sections.
• Phenotyping: Infers cell-type or tissue phenotypes from spatial expression profiles.
• Spatial analyses: Performs multiple spatial analyses, including identification of spatial gene expression patterns and enrichments.
• Comparative analysis: Enables comparative studies across samples to assess biological variation.
• Technology support: Accepts outputs from Space Ranger Visium and CosMx and tabular formats containing expression data paired with spatial coordinates.
• Community tool integration: Integrates SpaGCN, STdeconvolve, and InSituType for specialized spatial analyses.
• R package foundation: Built on the spatialGE R package.

Scientific Applications:

• Melanoma brain metastasis tumor microenvironment: Applied to identify spatial gene expression patterns and enrichments within melanoma brain metastasis samples.
• Merkel cell carcinoma: Used to detect spatial expression patterns and enrichments in Merkel cell carcinoma tissue.

Methodology:

Built on the spatialGE R package and integrating SpaGCN, STdeconvolve, and InSituType, with pipelines for quality control, normalization, domain detection, phenotyping, and spatial analyses; supports Space Ranger Visium, CosMx, and tabular expression-plus-coordinate inputs.