DOI: 10.18129/B9.bioc.HCAData  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HCAData.

Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor

Bioconductor version: 3.16

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/).

Author: Federico Marini [aut, cre]

Maintainer: Federico Marini <marinif at uni-mainz.de>

Citation (from within R, enter citation("HCAData")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Accessing the Human Cell Atlas datasets
PDF   Reference Manual
Text   NEWS


biocViews ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SingleCellData
Version 1.14.0
License MIT + file LICENSE
Depends R (>= 3.6), SingleCellExperiment
Imports ExperimentHub, AnnotationHub, HDF5Array, utils
Suggests knitr, rmarkdown, BiocStyle, scran(>= 1.11.4), BiocSingular, scater, scuttle, Rtsne, igraph, iSEE, testthat
URL https://github.com/federicomarini/HCAData
Depends On Me OSCA.workflows
Imports Me
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package HCAData_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HCAData
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HCAData
Package Short Url https://bioconductor.org/packages/HCAData/
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