## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("SingleCellMultiModal") ## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------ library(SingleCellMultiModal) library(MultiAssayExperiment) ## ----------------------------------------------------------------------------- scNMT("mouse_gastrulation", mode = "*", version = "1.0.0", dry.run = TRUE) ## ----------------------------------------------------------------------------- scNMT("mouse_gastrulation", version = "1.0.0") ## ----------------------------------------------------------------------------- scNMT("mouse_gastrulation", version = '2.0.0', dry.run = TRUE) ## ----message=FALSE------------------------------------------------------------ nmt <- scNMT("mouse_gastrulation", mode = c("*_DHS", "*_cgi", "*_genebody"), version = "1.0.0", dry.run = FALSE) nmt ## ----------------------------------------------------------------------------- colData(nmt) ## ----------------------------------------------------------------------------- rownames(nmt) ## ----------------------------------------------------------------------------- sampleMap(nmt) ## ----------------------------------------------------------------------------- colnames(nmt) ## ----------------------------------------------------------------------------- head(assay(nmt, "acc_DHS"))[, 1:4] ## ----------------------------------------------------------------------------- head(assay(nmt, "met_DHS"))[, 1:4] ## ----------------------------------------------------------------------------- sessionInfo()