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- Larsson, Ludvig, et al.
(författare)
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Semla : a versatile toolkit for spatially resolved transcriptomics analysis and visualization
- 2023
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 39:10
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Tidskriftsartikel (refereegranskat)abstract
- SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The 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/.
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