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

Queries the Human Cell Atlas

Bioconductor version: Development (3.20)

Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.

Author: Stefano Mangiola [aut, cre, rev] , Michael Milton [aut, rev] , Martin Morgan [ctb, rev], Vincent Carey [ctb, rev], Julie Iskander [rev], Tony Papenfuss [rev], Silicon Valley Foundation CZF2019-002443 [fnd], NIH NHGRI 5U24HG004059-18 [fnd], Victoria Cancer Agency ECRF21036 [fnd], NHMRC 1116955 [fnd]

Maintainer: Stefano Mangiola <mangiolastefano at>

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


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:

CuratedAtlasQueryR HTML R Script
Reference Manual PDF


biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.3.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-3
Depends R (>= 4.2.0)
Imports dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr
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Suggests zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot
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Follow Installation instructions to use this package in your R session.

Source Package CuratedAtlasQueryR_1.3.0.tar.gz
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macOS Binary (x86_64) CuratedAtlasQueryR_1.3.0.tgz
macOS Binary (arm64) CuratedAtlasQueryR_1.3.0.tgz
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