concordexR

Description

Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.

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People

• Kayla Jackson author maintainer
• A. Sina Booeshaghi author
• Angel Galvez-Merchan author
• Alexandra Kim contributor
• Laura Luebbert contributor
• Lambda Moses author
• Lior Pachter author rev ths