SPANIEL: Spatial Analysis: Integrating, Expression data with Location
Author(s): Rachel Queen,Adrienne Unsworth,Lefteris Zormpas,Simon Cockell
Affiliation(s): Newcastle University
Social media: https://twitter.com/rachelq_ncl
Spatial transcriptomics has the potential to revolutionise our understanding of many aspects of biology. The datasets, however, can be cumbersome to analyse and it can be difficult to navigate a field where many new specialised tools are regularly released. Here we present Spaniel; an R package with Shiny app designed to interactively share analysed data between the computational biologist other researchers in the group. Spaniel has been in Bioconductor since 2019 and we are currently adding functionality to the package, on the development branch for release in Bioconductor 3.18. The current version of Spaniel utilises a SpatialFeatureExperiment object which provides interoperability with other spatial transcriptomics analysis packages within the Bioconductor community. The Shiny app enables the selection of specific regions of tissue – allowing the researcher’s histological expertise to be used to define regions of interest to compare for further statistical analysis. We are actively working to increase the functionality of the Shiny app, to provide further tools to utilize the histological data, and to increase support for emerging analysis methods and new spatial transcriptomics technologies. We are seeking collaborators and input from the wider Bioconductor community.