{ "_id": "6a291124732311cd87596803", "Type": "Package", "Package": "cellNexus", "Title": "Queries the Human Cell Atlas", "Version": "0.99.23", "Authors@R": "c(\nperson(\n\"Stefano\",\n\"Mangiola\",\nemail = \"mangiolastefano@gmail.com\",\nrole = c(\"aut\", \"rev\", \"ctb\"),\ncomment = c(ORCID = \"0000-0001-7474-836X\")\n),\nperson(\n\"Mengyuan\",\n\"Shen\",\nemail = \"shen.m@wehi.edu.au\",\nrole = c(\"aut\", \"cre\", \"rev\"),\ncomment = c(ORCID = \"0009-0008-0057-8239\")\n),\nperson(\n\"Michael\",\n\"Milton\",\nemail = \"milton.m@wehi.edu.au\",\nrole = c(\"aut\", \"rev\", \"ctb\"),\ncomment = c(ORCID = \"0000-0002-8965-2595\")\n),\nperson(\n\"Jared\",\n\"Andrews\",\nemail = \"jared.andrews07@gmail.com\",\nrole = c(\"aut\", \"rev\", \"ctb\")\n),\nperson(\n\"Juan\",\n\"Henao\",\nemail = \"juan.henao@helmholtz-muenchen.de\",\nrole = c(\"aut\", \"ctb\")\n),\nperson(\n\"Edward\",\n\"Yang\",\nemail = \"edwardyang125@gmail.com\",\nrole = c(\"aut\", \"ctb\")\n),\nperson(\n\"Julie\",\n\"Iskander\",\nemail = \"iskander.j@wehi.edu.au\",\nrole = c( \"rev\")\n),\nperson(\n\"Silicon Valley Foundation\",\n\"CZF2019-002443\",\nrole = c( \"fnd\")\n),\nperson(\n\"NIH NHGRI\",\n\"5U24HG004059-18\",\nrole = c( \"fnd\")\n),\nperson(\n\"Victoria Cancer Agency\",\n\"ECRF21036\",\nrole = c( \"fnd\")\n),\nperson(\n\"NHMRC\",\n\"1116955\",\nrole = c( \"fnd\")\n))", "Description": "Provides access to a copy of the Human Cell Atlas, but\nwith harmonised metadata. This allows for uniform querying\nacross numerous datasets within the Atlas using common fields\nsuch as cell type, tissue type, and patient ethnicity. Usage\ninvolves first querying the metadata table for cells of\ninterest, and then downloading the corresponding cells into one\nof several supported formats, including SingleCellExperiment,\nSeurat, or pseudobulk SummarizedExperiment objects. Note: The\nHuman Cell Atlas data accessed through this package is subject\nto its own licensing terms (typically Creative Commons\nAttribution or similar open data licenses as specified by the\nHuman Cell Atlas Data Use Agreement), which differ from the\npackage license (GPL-3). See the package documentation for\ndetails.", "License": "GPL-3", "Biarch": "true", "biocViews": "AssayDomain, Infrastructure, SingleCell, RNASeq,\nDifferentialExpression, GeneExpression, Normalization,\nClustering, QualityControl, Sequencing, Transcription,\nTranscriptomics, ShinyApps", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "URL": "https://github.com/MangiolaLaboratory/cellNexus,\nhttps://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'\n'interface_app.R' 'metadata.R' 'seurat.R' 'unharmonised.R'\n'zzz.R'", "Language": "en-US", "SystemRequirements": "Python", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-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", 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