## ----setup, include = FALSE------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## -------------------------------------------------------------------------- suppressPackageStartupMessages({ library(ExperimentHub) library(SingleCellExperiment) library(TabulaMurisData) }) eh <- ExperimentHub() query(eh, "TabulaMurisData") ## -------------------------------------------------------------------------- droplet <- eh[["EH1617"]] droplet droplet <- TabulaMurisDroplet() droplet ## -------------------------------------------------------------------------- set.seed(1234) se <- droplet[, sample(seq_len(ncol(droplet)), 250, replace = FALSE)] se ## -------------------------------------------------------------------------- se <- scran::computeSumFactors(se) se <- scater::normalize(se) se <- scater::runPCA(se) se <- scater::runTSNE(se) ## ---- eval=FALSE----------------------------------------------------------- # if (require(iSEE)) { # iSEE(se) # } ## -------------------------------------------------------------------------- sessionInfo()