## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("SingleCellMultiModal") ## ---- include=TRUE, results="hide", message=FALSE, warning=FALSE-------------- library(MultiAssayExperiment) library(SingleCellMultiModal) ## ----------------------------------------------------------------------------- CITEseq(DataType="peripheral_blood", modes="*", dry.run=TRUE, version="1.0.0") ## ----message=FALSE------------------------------------------------------------ mae <- CITEseq(DataType="peripheral_blood", modes="*", dry.run=FALSE, version="1.0.0") mae ## ----------------------------------------------------------------------------- experiments(mae) ## ----------------------------------------------------------------------------- rownames(mae) ## ----------------------------------------------------------------------------- sampleMap(mae) ## ----------------------------------------------------------------------------- head(experiments(mae)$scRNA)[, 1:4] ## ----------------------------------------------------------------------------- head(experiments(mae)$scADT)[, 1:4] ## ----------------------------------------------------------------------------- (ctclMae <- mae[,colData(mae)$condition == "CTCL",]) ## ----------------------------------------------------------------------------- ctclMae[,complete.cases(ctclMae),] ## ----------------------------------------------------------------------------- sgRNAs <- metadata(mae) names(sgRNAs) ## ----------------------------------------------------------------------------- head(sgRNAs$CTCL_TCRab) ## ----message=FALSE------------------------------------------------------------ sce <- CITEseq(DataType="peripheral_blood", modes="*", dry.run=FALSE, version="1.0.0", DataClass="SingleCellExperiment") sce ## ---- tidy=TRUE--------------------------------------------------------------- sessionInfo()