knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
The TabulaMurisData
data package provides access to the 10x and SmartSeq2
single-cell RNA-seq data sets from
the Tabula Muris Consortium.
The contents of the package can be seen by querying the ExperimentHub for the
package name.
suppressPackageStartupMessages({ library(ExperimentHub) library(SingleCellExperiment) library(TabulaMurisData) }) eh <- ExperimentHub() query(eh, "TabulaMurisData")
The individual data sets can be accessed using either their ExperimentHub accession number, or the convenience functions provided in this package. For example, for the 10x data:
droplet <- eh[["EH1617"]] droplet droplet <- TabulaMurisDroplet() droplet
iSEE
Each data set is provided in the form of a SingleCellExperiment
object. To
gain further insights into the contents of the data sets, they can be explored
using, e.g., the r Biocpkg("iSEE")
package. For the purposes of this vignette,
we first subsample a small subset of the cells in the 10x data set, to reduce
the run time.
set.seed(1234) se <- droplet[, sample(seq_len(ncol(droplet)), 250, replace = FALSE)] se
Next, we calculate size factors and normalize the data using the
r Biocpkg("scran")
and r Biocpkg("scater")
packages, and perform dimension
reduction using PCA and t-SNE.
se <- scran::computeSumFactors(se) se <- scater::logNormCounts(se) se <- scater::runPCA(se) se <- scater::runTSNE(se)
Finally, we call iSEE
with the subsampled SingleCellExperiment
object. This
opens up an instance of iSEE
containing the provided data set.
if (require(iSEE)) { iSEE(se) }
sessionInfo()
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