CuratedAtlasQueryR
Queries the Human Cell Atlas
Bioconductor version: 3.23 · Package version: 1.10.0
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 gmail.com>
Citation
From within R, enter citation("CuratedAtlasQueryR"):
Stefano Mangiola, Michael Milton. CuratedAtlasQueryR: Queries the Human Cell Atlas. doi:10.18129/B9.bioc.CuratedAtlasQueryR, R package version 1.10.0, https://bioconductor.org/packages/CuratedAtlasQueryR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CuratedAtlasQueryR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.10.0 |
| License | GPL-3 |
| URL | https://github.com/stemangiola/CuratedAtlasQueryR |
| Bug Reports | https://github.com/stemangiola/CuratedAtlasQueryR/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| Status | Deprecated |
| Downloads rank | 2284 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/CuratedAtlasQueryR/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CuratedAtlasQueryR")| CuratedAtlasQueryR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | CuratedAtlasQueryR_1.10.0.tar.gz |
| Windows binary (x86_64) | CuratedAtlasQueryR_1.10.0.zip |
| macOS binary (arm64) | CuratedAtlasQueryR_1.10.0.tgz |
| macOS binary (x86_64) | CuratedAtlasQueryR_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CuratedAtlasQueryR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CuratedAtlasQueryR |
| Package Downloads Report | Download Stats |
Dependencies
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
Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot