{"entity": "publication", "iuid": "c3e177c65cc745ac9759e39cfda5681b", "timestamp": "2026-08-20T20:53:37.391Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c3e177c65cc745ac9759e39cfda5681b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c3e177c65cc745ac9759e39cfda5681b"}}, "title": "Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.", "authors": [{"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L", "orcid": "0000-0003-3755-718X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/496c1998b3dd4c33a89b38bed7dea4d1.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "journal article", "published": "2023-10-03", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "39", "issue": "10", "issn-l": "1367-4803"}, "abstract": "Spatially resolved transcriptomics technologies generate gene expression data with retained positional information from a tissue section, often accompanied by a corresponding histological image. Computational tools should make it effortless to incorporate spatial information into data analyses and present analysis results in their histological context. Here, we present semla, an R package for processing, analysis, and visualization of spatially resolved transcriptomics data generated by the Visium platform, that includes interactive web applications for data exploration and tissue annotation.\n\nThe R package semla is available on GitHub (https://github.com/ludvigla/semla), under the MIT License, and deposited on Zenodo (https://doi.org/10.5281/zenodo.8321645). Documentation and tutorials with detailed descriptions of usage can be found at https://ludvigla.github.io/semla/.", "doi": "10.1093/bioinformatics/btad626", "pmid": "37846051", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10597621"}, {"db": "pii", "key": "7319366"}], "notes": [], "created": "2026-08-20T09:39:40.270Z", "modified": "2026-08-20T09:39:40.352Z"}