Introduction to cellxgenedp

The cellxgene data portal https://cellxgene.cziscience.com/ provides a graphical user interface to collections of single-cell sequence data processed in standard ways to ‘count matrix’ summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.

Installation

This package is available in Bioconductor version 3.15 and later. The following code installs cellxgenedp

if (!"BiocManager" %in% rownames(installed.packages()))
    install.packages("BiocManager", repos = "https://CRAN.R-project.org")
BiocManager::install("cellxgenedp")

Alternatively, install the ‘development’ version from GitHub

if (!"remotes" %in% rownames(installed.packages()))
    install.packages("remotes", repos = "https://CRAN.R-project.org")
remotes::install_github("mtmorgan/cellxgenedp")

To also install additional packages required for this vignette, use

pkgs <- c("tidyr", "zellkonverter", "SingleCellExperiment", "HDF5Array")
required_pkgs <- pkgs[!pkgs %in% rownames(installed.packages())]
BiocManager::install(required_pkgs)

Use

Load the package into your current R session. We make extensive use of the dplyr packages, and at the end of the vignette use SingleCellExperiment and zellkonverter, so load those as well.

suppressPackageStartupMessages({
    library(dplyr)
    library(cellxgenedp)
})

Shiny

cxg() provides a ‘shiny’ interface allowing discovery of collections and datasets, visualization of selected datasets in the cellxgene data portal, and download of datasets for use in R.

Next steps

View the artcle Discover and download datasets and files from the cellxgene data portal.