Monkeybread: A Python toolkit for the analysis of cellular niches in single-cell resolution spatial transcriptomics data

• DOI: 10.1101/2023.09.14.557736
• Publication Date: 2023-09-15T14:05:23Z
• Authors: Matthew N. Bernstein; Dillon Scott; Cynthia C. Hession; Tim Nieuwenhuis; Jacqueline Gerritsen; Siamak Tabrizi; Vandana Nandivada; Matthew A. Huggins; Meixue Duan; Shruti Malu; Ming Tang
• Keywords: Python

Summary Spatial transcriptomics technologies enable the spatially resolved measurement of gene expression within a tissue specimen. With these technologies, researchers can investigate how cells organize into cellular niches which are defined as distinct regions in comprising specific composition cell types or phenotypes. While general-purpose software tools for exploratory analysis spatial data exist, there is need that specialize organization niches. This further enhance downstream application towards drug target discovery, validation, and biomarker development. We present Monkeybread: A Python toolkit analyzing intercellular communication single-cell resolution data. applied Monkeybread to human melanoma sample demonstrate its utility identifying with diverse immunogenic compositions tumor microenvironment. found were differentially enriched tolerogenic macrophage populations could be correlated T abundance. These findings highlight used revealing underlying biology microenvironment, future, understanding influence on response available treatments discovery novel targets.