SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.
SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.
Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")SuperSpot can be installed with the command:
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")An example vignette is available (see example). The code used to produce the figures of the application note can be found here.