## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # install.packages("BiocManager") # BiocManager::install("STexampleData") ## ----eval=FALSE--------------------------------------------------------------- # install.packages("remotes") # remotes::install_github("lmweber/STexampleData", build_vignettes = TRUE) ## ----message=FALSE------------------------------------------------------------ library(SpatialExperiment) library(STexampleData) ## ----message=FALSE------------------------------------------------------------ # load object spe <- Visium_humanDLPFC() # check object spe dim(spe) assayNames(spe) rowData(spe) colData(spe) head(spatialCoords(spe)) imgData(spe) ## ----message=FALSE------------------------------------------------------------ # load object spe <- Visium_mouseCoronal() # check object spe ## ----message=FALSE------------------------------------------------------------ # load object spe <- seqFISH_mouseEmbryo() # check object spe ## ----message=FALSE------------------------------------------------------------ # load object spe <- ST_mouseOB() # check object spe ## ----message=FALSE------------------------------------------------------------ # load object spe <- SlideSeqV2_mouseHPC() # check object spe ## ----message=FALSE------------------------------------------------------------ library(ExperimentHub) ## ----message=FALSE------------------------------------------------------------ # create ExperimentHub instance eh <- ExperimentHub() # query STexampleData datasets myfiles <- query(eh, "STexampleData") myfiles # metadata md <- as.data.frame(mcols(myfiles)) ## ----message=FALSE------------------------------------------------------------ # load Visium_humanDLPFC dataset using ExperimentHub query spe <- myfiles[[1]] spe ## ----message=FALSE------------------------------------------------------------ # load Visium_humanDLPFC dataset using ExperimentHub ID spe <- myfiles[["EH7538"]] spe ## ----------------------------------------------------------------------------- sessionInfo()