Type: Package
Package: CuratedAtlasQueryR
Title: Queries the Human Cell Atlas
Version: 1.10.0
Authors@R: c(
    person(
        "Stefano",
        "Mangiola",
        email = "mangiolastefano@gmail.com",
        role = c("aut", "cre", "rev"),
        comment = c(ORCID = "0000-0001-7474-836X")
    ),
    person(
        "Michael",
        "Milton",
        email = "milton.m@wehi.edu.au",
        role = c("aut", "rev"),
        comment = c(ORCID = "0000-0002-8965-2595")
    ),
    person(
        "Martin",
        "Morgan",
        email = "Martin.Morgan@RoswellPark.org",
        role = c("ctb", "rev")
    ),
    person(
        "Vincent",
        "Carey",
        email = "stvjc@channing.harvard.edu",
        role = c("ctb", "rev")
    ),
    person(
        "Julie",
        "Iskander",
        email = "iskander.j@wehi.edu.au",
        role = c( "rev")
    ),
    person(
        "Tony",
        "Papenfuss",
        email = "papenfuss@wehi.edu.au",
        role = c( "rev")
    ),
    person(
        "Silicon Valley Foundation",
        "CZF2019-002443",
        role = c( "fnd")
    ),
    person(
        "NIH NHGRI",
        "5U24HG004059-18",
        role = c( "fnd")
    ),
    person(
        "Victoria Cancer Agency",
        "ECRF21036",
        role = c( "fnd")
    ),
    person(
        "NHMRC",
        "1116955",
        role = c( "fnd")
    ))
Description: 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.
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
Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow,
        reticulate, spelling, forcats, ggplot2,
        tidySingleCellExperiment, rprojroot
Biarch: true
biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression,
        GeneExpression, Normalization, Clustering, QualityControl,
        Sequencing, Transcription, Transcriptomics
Encoding: UTF-8
RoxygenNote: 7.2.3
URL: https://github.com/stemangiola/CuratedAtlasQueryR
BugReports: https://github.com/stemangiola/CuratedAtlasQueryR/issues
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Collate: 'utils.R' 'counts.R' 'dev.R' 'metadata.R' 'seurat.R'
        'unharmonised.R' 'zzz.R'
Language: en-US
PackageStatus: Deprecated
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 13:01:11 UTC
RemoteUrl: https://github.com/bioc/CuratedAtlasQueryR
RemoteRef: RELEASE_3_23
RemoteSha: 553d9afbb96a328a235f491078a3b237d042f9cd
NeedsCompilation: no
Packaged: 2026-11-07 11:04:54 UTC; root
Author: Stefano Mangiola [aut, cre, rev] (ORCID:
    <https://orcid.org/0000-0001-7474-836X>),
  Michael Milton [aut, rev] (ORCID:
    <https://orcid.org/0000-0002-8965-2595>),
  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@gmail.com>