Type: Package
Package: cellNexus
Title: Queries the Human Cell Atlas
Version: 0.99.23
Authors@R: c(
    person(
        "Stefano",
        "Mangiola",
        email = "mangiolastefano@gmail.com",
        role = c("aut", "rev", "ctb"),
        comment = c(ORCID = "0000-0001-7474-836X")
    ),
    person(
        "Mengyuan",
        "Shen",
        email = "shen.m@wehi.edu.au",
        role = c("aut", "cre", "rev"),
        comment = c(ORCID = "0009-0008-0057-8239")
    ),
    person(
        "Michael",
        "Milton",
        email = "milton.m@wehi.edu.au",
        role = c("aut", "rev", "ctb"),
        comment = c(ORCID = "0000-0002-8965-2595")
    ),
    person(
        "Jared",
        "Andrews",
        email = "jared.andrews07@gmail.com",
        role = c("aut", "rev", "ctb")
    ),
    person(
        "Juan",
        "Henao",
        email = "juan.henao@helmholtz-muenchen.de",
        role = c("aut", "ctb")
    ),
    person(
        "Edward",
        "Yang",
        email = "edwardyang125@gmail.com",
        role = c("aut", "ctb")
    ),
    person(
        "Julie",
        "Iskander",
        email = "iskander.j@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 one
        of several supported formats, including SingleCellExperiment,
        Seurat, or pseudobulk SummarizedExperiment objects. Note: The
        Human Cell Atlas data accessed through this package is subject
        to its own licensing terms (typically Creative Commons
        Attribution or similar open data licenses as specified by the
        Human Cell Atlas Data Use Agreement), which differ from the
        package license (GPL-3). See the package documentation for
        details.
License: GPL-3
Depends: R (>= 4.5.0)
Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>=
        1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, curl,
        cli, SeuratObject, Seurat, methods, rlang, S4Vectors, tibble,
        utils, dbplyr (>= 2.3.0), duckdb, checkmate, shiny,
        shinyWidgets, zellkonverter, anndataR, stringr, Matrix,
        rclipboard
Suggests: BiocStyle, knitr, rmarkdown, testthat, basilisk, arrow,
        reticulate, spelling, forcats, ggplot2, rprojroot, openssl,
        DelayedArray, tidybulk, BiocParallel, preprocessCore
Biarch: true
biocViews: AssayDomain, Infrastructure, SingleCell, RNASeq,
        DifferentialExpression, GeneExpression, Normalization,
        Clustering, QualityControl, Sequencing, Transcription,
        Transcriptomics, ShinyApps
Encoding: UTF-8
RoxygenNote: 7.3.3
URL: https://github.com/MangiolaLaboratory/cellNexus,
        https://mangiolalaboratory.github.io/cellNexus/
BugReports: https://github.com/MangiolaLaboratory/cellNexus/issues
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Collate: 'utils.R' 'counts.R' 'counts_per_million.R' 'data.R' 'dev.R'
        'interface_app.R' 'metadata.R' 'seurat.R' 'unharmonised.R'
        'zzz.R'
Language: en-US
SystemRequirements: Python
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-26 07:15:53 UTC
RemoteUrl: https://github.com/bioc/cellNexus
RemoteRef: HEAD
RemoteSha: d7f0137d1c71be379107844554c6370f3a1b6ffe
NeedsCompilation: no
Packaged: 2026-06-10 07:13:05 UTC; root
Author: Stefano Mangiola [aut, rev, ctb] (ORCID:
    <https://orcid.org/0000-0001-7474-836X>),
  Mengyuan Shen [aut, cre, rev] (ORCID:
    <https://orcid.org/0009-0008-0057-8239>),
  Michael Milton [aut, rev, ctb] (ORCID:
    <https://orcid.org/0000-0002-8965-2595>),
  Jared Andrews [aut, rev, ctb],
  Juan Henao [aut, ctb],
  Edward Yang [aut, ctb],
  Julie Iskander [rev],
  Silicon Valley Foundation CZF2019-002443 [fnd],
  NIH NHGRI 5U24HG004059-18 [fnd],
  Victoria Cancer Agency ECRF21036 [fnd],
  NHMRC 1116955 [fnd]
Maintainer: Mengyuan Shen <shen.m@wehi.edu.au>