## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("SingleCellMultiModal") ## ----include=TRUE, results="hide", message=FALSE, warning=FALSE--------------- library(MultiAssayExperiment) library(SpatialExperiment) library(SingleCellMultiModal) ## ----------------------------------------------------------------------------- seqFISH( DataType="mouse_visual_cortex", modes="*", dry.run=TRUE, version="2.0.0" ) ## ----------------------------------------------------------------------------- seqfish <- seqFISH( DataType="mouse_visual_cortex", modes="*", dry.run=FALSE, version="2.0.0" ) seqfish ## ----------------------------------------------------------------------------- experiments(seqfish) ## ----------------------------------------------------------------------------- rownames(seqfish) ## ----------------------------------------------------------------------------- sampleMap(seqfish) ## ----------------------------------------------------------------------------- upsetSamples(seqfish) ## ----------------------------------------------------------------------------- seqfish[["scRNAseq"]] ## ----------------------------------------------------------------------------- head(assay(seqfish, "scRNAseq"))[,1:4] ## ----------------------------------------------------------------------------- seqfish[["seqFISH"]] ## ----------------------------------------------------------------------------- head(assay(seqfish, "seqFISH"))[,1:4] ## ----------------------------------------------------------------------------- (sd <- spatialData(seqfish[["seqFISH"]])) ## ----------------------------------------------------------------------------- head(sc <- spatialCoords(seqfish[["seqFISH"]])) ## ----------------------------------------------------------------------------- spatialCoordsNames(seqfish[["seqFISH"]]) ## ----------------------------------------------------------------------------- seqFISH( DataType="mouse_visual_cortex", modes="*", dry.run=FALSE, version="1.0.0" ) ## ----tidy=TRUE---------------------------------------------------------------- sessionInfo()