Package 'HCAData'

Title: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor
Description: This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/).
Authors: Federico Marini [aut, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
Maintainer: Federico Marini <[email protected]>
License: MIT + file LICENSE
Version: 1.28.0
Built: 2026-10-10 11:15:22 UTC
Source: https://github.com/bioc/HCAData

Help Index

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")