HCAData: Download data from the HCA via ExperimentHub

In federicomarini/HCAData: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor

Download data from the HCA via ExperimentHub

Description

Download HDF5 (dense assay) and RDS (row and column annotations) files from the HCA via ExperimentHub, composing them together as a SingleCellExperiment object

Usage

HCAData(dataset = NULL, as.sparse = TRUE)

Arguments

dataset	A character string: which dataset should be retrieved?
as.sparse	Logical, specifies whether the underlying HDF5 dataset should be treated as sparse or not - will be passed to the call to 'HDF5Array()'. Defaults to TRUE, i.e. by using the 'DelayedArray' infrastructure.

Details

This current release includes the following datasets:

Census of Immune Cells - Umbilical cord blood

UMI counts from the 10x (droplet) single-cell RNA-seq data. The object contains counts for 33694 genes in 384000 cells.

Census of Immune Cells - Bone marrow

UMI counts from the 10x (droplet) single-cell RNA-seq data. The object contains counts for 33694 genes in 378000 cells.

Value

A SingleCellExperiment object with a HDF5Matrix in the counts assay, containing the UMI counts for each gene in each cell. Row- and column-level metadata are also provided.

Examples

HCAData()
sce_cordblood <- HCAData("ica_cord_blood")

federicomarini/HCAData documentation built on May 5, 2024, 1:24 p.m.