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R package of CZ CELLxGENE Discover Census

This is the documentation for the R package cellxgene.census which is part of CZ CELLxGENE Discover Census. For full details on Census data and capabilities please go to the main Census site.

cellxgene.census provides an API to efficiently access the cloud-hosted Census single-cell data from R. In just a few seconds users can access any slice of Census data using cell or gene filters across hundreds of single-cell datasets.

Census data can be fetched in an iterative fashion for bigger-than-memory slices of data, or quickly exported to basic R structures, as well as Seurat or SingleCellExperiment objects for downstream analysis.

Installation

If installing from Ubuntu, you may need to install the following libraries via apt install, libxml2-dev libssl-dev libcurl4-openssl-dev. In addition you must have cmake v3.21 or greater.

If installing from MacOS, you will need to install the developer tools Xcode.

Windows is not supported.

Then in an R session install cellxgene.census from R-Universe.

install.packages(
  "cellxgene.census",
  repos=c('https://chanzuckerberg.r-universe.dev', 'https://cloud.r-project.org')
)

To be able to export Census data to Seurat or SingleCellExperiment you also need to install their respective packages.

# Seurat
install.packages("Seurat")

# SingleCellExperiment
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleCellExperiment")

Usage

Check out the vignettes in the “Articles” section of the navigation bar on this site. We highly recommend the following vignettes as a starting point:

You can also check out out the quick start guide in the main Census site.

Example Seurat and SingleCellExperiment query

The following creates a Seurat object on-demand with all sympathetic neurons in Census and filtering only for the genes ENSG00000161798, ENSG00000188229.

library("cellxgene.census")
library("Seurat")

census <- open_soma()

organism <- "Homo sapiens"
gene_filter <- "feature_id %in% c('ENSG00000107317', 'ENSG00000106034')"
cell_filter <-  "cell_type == 'sympathetic neuron'"
cell_columns <- c("assay", "cell_type", "tissue", "tissue_general", "suspension_type", "disease")

seurat_obj <- get_seurat(
   census = census,
   organism = organism,
   var_value_filter = gene_filter,
   obs_value_filter = cell_filter,
   obs_column_names = cell_columns
)

And the following retrieves the same data as a SingleCellExperiment object.

library("SingleCellExperiment")

sce_obj <- get_single_cell_experiment(
   census = census,
   organism = organism,
   var_value_filter = gene_filter,
   obs_value_filter = cell_filter,
   obs_column_names = cell_columns
)

For More Help

For more help, please go visit the main Census site.

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