{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide , SA 5005,",
    "Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, Melbourne, Victoria 3052,",
    "Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne , Parkville, VIC 3010,",
    "South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, SA 5005,",
    "SAiGENCI",
    "Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia",
    "Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia",
    "The Walter and Eliza Hall Institute of Medical Research",
    "Frazer Institute, Faculty of Medicine, The University of Queensland , Brisbane, Queensland 4102,",
    "The University of Queensland",
    "Walter and Eliza Hall Institute of Medical Research",
    "Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia",
    "Department of Anatomy and Developmental Biology, Monash University , Clayton, VIC 3800,",
    "Computational Biology, Isomorphic Labs , Bishopsgate, London, EC2M 4RB,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0,
        1,
        2,
        3,
        4
      ],
      "name": "Ning Liu",
      "orcid": "0000-0002-9487-9305"
    },
    {
      "affs": [
        1,
        2,
        5,
        6
      ],
      "name": "Jarryd Martin"
    },
    {
      "affs": [
        1,
        2,
        3,
        4
      ],
      "name": "Dharmesh Dinesh Bhuva",
      "orcid": "0000-0002-6398-9157"
    },
    {
      "affs": [
        1,
        2,
        5,
        6
      ],
      "name": "Jinjin Chen",
      "orcid": "0000-0001-7923-5723"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Mengbo Li",
      "orcid": "0000-0002-9666-5810"
    },
    {
      "affs": [
        1,
        2,
        5,
        6
      ],
      "name": "Sam Lee",
      "orcid": "0000-0002-6805-4051"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Malvika Kharbanda",
      "orcid": "0000-0001-9726-3023"
    },
    {
      "affs": [
        1,
        2,
        5,
        6
      ],
      "name": "Jinming Cheng",
      "orcid": "0000-0003-3806-4694"
    },
    {
      "affs": [
        1,
        2,
        7
      ],
      "name": "Ahmed Mohamed",
      "orcid": "0000-0001-6507-5300"
    },
    {
      "affs": [
        8,
        9
      ],
      "name": "Arutha Kulasinghe",
      "orcid": "0000-0003-3224-7350"
    },
    {
      "affs": [
        1,
        2,
        10
      ],
      "name": "Yunshun Chen",
      "orcid": "0000-0003-4911-5653"
    },
    {
      "affs": [
        1,
        2,
        8,
        5,
        6,
        11
      ],
      "name": "Chin Wee Tan",
      "orcid": "0000-0001-9695-7218"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Fuyi Li"
    },
    {
      "affs": [
        0,
        12,
        3
      ],
      "name": "Jose Maria Polo",
      "orcid": "0000-0002-2531-778X"
    },
    {
      "affs": [
        1,
        13,
        2,
        3
      ],
      "name": "Melissa J. Davis",
      "orcid": "0000-0003-4864-7033"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ba6ve8czh99t2.bib",
  "cited_by": 11,
  "doi": "10.1093/bioinformatics/btag609",
  "fulltext_url": null,
  "id": "ba6ve8czh99t2",
  "issns": [
    "1367-4803",
    "1367-4811"
  ],
  "landing_url": "https://doi.org/10.1093/bioinformatics/btag609",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
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  "openalex": "W4393307128",
  "pdf_url": null,
  "pmcid": "PMC13503035",
  "pmid": "42596574",
  "published": "2026-08-01",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/ba6ve8czh99t2.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:46Z",
      "native_id": "W4393307128",
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      "url": "https://doi.org/10.1093/bioinformatics/btag609"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data",
  "title_text": "hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T13:20:43Z",
  "url": "https://research.draconitic.com/paper/ba6ve8czh99t2",
  "venue": "Bioinformatics",
  "versions": []
}