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This is the development version of HCATonsilData; for the stable release version, see HCATonsilData.

Provide programmatic access to the tonsil cell atlas datasets

Bioconductor version: Development (3.20)

This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.

Author: Ramon Massoni-Badosa [aut, cre] , Federico Marini [aut] , Alan O'Callaghan [aut], Helena L. Crowell [aut]

Maintainer: Ramon Massoni-Badosa <ramonmassoni at>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

HCATonsilData HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SingleCellData, SpatialData
Version 1.3.0
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports ExperimentHub, SingleCellExperiment, SpatialExperiment, HDF5Array, SummarizedExperiment, S4Vectors, htmltools, rmarkdown, base64enc, utils
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Suggests knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package HCATonsilData_1.3.0.tar.gz
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