concordexR

concordexR identifies spatial homogeneous regions (SHRs) in tissues by analyzing k-nearest-neighbor (kNN) graphs constructed from spatial transcriptomics data to detect domains homogenous with respect to cell type composition.

Key Features:

• Spatial Homogeneous Region Detection: Identifies SHRs in tissues that are homogenous with respect to cell type composition using spatial transcriptomics data.
• k-Nearest-Neighbor Graph Analysis: Relies on analysis of kNN graphs to detect spatial patterns and regional homogeneity.
• Non-Spatial Transcriptomics Support: Analyzes non-spatial transcriptomics data to assess concordance between cell partitions from clustering algorithms and transcriptomic similarity in kNN graphs.
• Cross-Tissue Applicability: Efficiently finds SHRs across a wide variety of tissue types.

Scientific Applications:

• Spatial Transcriptomics Analysis: Identifies spatial homogeneous regions in tissue samples based on cell type composition.
• Clustering Validation: Evaluates the concordance between clustering algorithm partitions and transcriptomic similarity represented in kNN graphs.

Methodology:

concordexR analyzes k-nearest-neighbor (kNN) graphs constructed from transcriptomics data to identify spatial homogeneous regions and assess concordance between cell partitions and transcriptomic similarity.