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Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.

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/.

SUBMITTER: Larsson L

PROVIDER: S-EPMC10597621 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization.

Larsson Ludvig L Franzén Lovisa L Ståhl Patrik L PL Lundeberg Joakim J

Bioinformatics (Oxford, England) 20231001 10

<h4>Summary</h4>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 gener ...[more]

PMID: 37846051

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