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bioRxiv · 10.1101/2023.03.27.534291

i-stLearn: An interactive platform for spatial transcriptomics analysis

Pham, D.·Balderson, B.·Nguyen, Q.
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Abstract

SummaryEmerging spatial transcriptomics technologies (e.g. Visium, Slideseq, or MERFISH) have made it possible to keep the spatial information while profiling gene expression of every cell/spatial-spot. Integrating expression values, spatial coordinates, and imaging data type promises to bring more biological insights but is still technically challenging. A user-friendly software tool to enable interactive analysis of spatial transcriptomic data by the broader community is lacking. We present i-stLearn, an all-in-on web application with an analysis pipeline and interactive visualization for studying spatial heterogeneity using spatial transcriptomics data. i-stLearn can be used to gain biological insights from tissue through key analysis types cell-cell interaction analysis, clustering, and trajectory inference. Using functions, users can interactively segment the tissue and identify cellular state transition or cellular communications in a heterogeneous biological sample. Availabilityi-stLearn is freely available at https://github.com/BiomedicalMachineLearning/stlearn_interactive as local web application and we also provide a demo online web service available at https://i-stlearn-demo.web.app. Contactquan.nguyen@imb.uq.edu.au Supplementary informationSupplementary data are available at Bioinformatics online.

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Pham, D., Balderson, B., Nguyen, Q.. 2023-03-28. i-stLearn: An interactive platform for spatial transcriptomics analysis. https://doi.org/10.1101/2023.03.27.534291

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