hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data

Liu, N; Martin, J; Bhuva, DD; Chen, J; Li, M; Lee, SC; Kharbanda, M; Cheng, J; Mohamed, A; Kulasinghe, A; Chen, Y; Tan, CW; Li, F; Polo, JM; Davis, MJ

Author(s): Liu, N; Martin, J; Bhuva, DD; Chen, J; Li, M; Lee, SC; Kharbanda, M; Cheng, J; Mohamed, A; Kulasinghe, A; Chen, Y; Tan, CW; Li, F; Polo, JM; Davis, MJ;
Journal Title: Bioinformatics
Publication Type: Aug 13
Abstract: MOTIVATION: Understanding complex cellular neighborhoods has provided new insights into tissue biology. Accurate neighborhood identification is crucial, yet existing methods often focus on hard assignment and do not generate cell-specific neighborhood profiles at single-cell level. RESULTS: We developed hoodscanR, a Bioconductor package identifying and analyzing cellular neighborhoods in spatial data. The central output of hoodscanR is a cell-level neighborhood probability profile, which represents partial membership of each cell across multiple annotation-defined neighborhoods. This probabilistic representation supports downstream analyses including neighborhood visualization, uncertainty assessment, neighborhood-based clustering and neighborhood-aware differential expression. Applying hoodscanR to breast and lung cancer datasets, we showcase its ability to characterize mixed tissue environments and identify transcriptional changes in tumor cells from distinct spatial neighborhoods. AVAILABILITY: The hoodscanR package is publicly available in Bioconductor at https://bioconductor.org/packages/release/bioc/html/hoodscanR.html.
Publisher: Oxford Academic
Keywords: *Software; Spatial Transcriptomics; Humans; *Single-Cell Analysis/methods; Single-Cell Gene Expression Analysis; *Gene Expression Profiling/methods
Research Division(s): Bioinformatics and Computational Biology; Cancer Biology and Stem Cells; Immunology
PubMed ID: 42596574
Publisher's Version: https://doi.org/10.1093/bioinformatics/btag609
Open Access at Publisher's Site: https://doi.org/10.1093/bioinformatics/btag609
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2026-08-28 10:52:07

Last Modified: 2026-08-28 10:56:27