Package: CuratedAtlasQueryR 1.3.0
Stefano Mangiola
CuratedAtlasQueryR: Queries the Human Cell Atlas
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.
Authors:
CuratedAtlasQueryR_1.3.0.tar.gz
CuratedAtlasQueryR_1.3.0.zip(r-4.5)CuratedAtlasQueryR_1.3.0.zip(r-4.4)CuratedAtlasQueryR_1.3.0.zip(r-4.3)
CuratedAtlasQueryR_1.3.0.tgz(r-4.4-any)CuratedAtlasQueryR_1.3.0.tgz(r-4.3-any)
CuratedAtlasQueryR_1.3.0.tar.gz(r-4.5-noble)CuratedAtlasQueryR_1.3.0.tar.gz(r-4.4-noble)
CuratedAtlasQueryR_1.3.0.tgz(r-4.4-emscripten)CuratedAtlasQueryR_1.1.1.tgz(r-4.3-emscripten)
CuratedAtlasQueryR.pdf |CuratedAtlasQueryR.html✨
CuratedAtlasQueryR/json (API)
NEWS
| # Install 'CuratedAtlasQueryR' in R: |
| install.packages('CuratedAtlasQueryR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stemangiola/curatedatlasqueryr/issues
On BioConductor:CuratedAtlasQueryR-1.3.0(bioc 3.20)CuratedAtlasQueryR-1.2.0(bioc 3.19)
Last updated 2 months agofrom:73d995f68c
Exports:DATABASE_URLget_metadataget_seuratget_single_cell_experimentget_SingleCellExperimentget_unharmonised_metadataSAMPLE_DATABASE_URL
Dependencies:abindaskpassassertthatbase64encBHBiobaseBiocGenericsbitopsblobbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdotCall64dplyrdqrngduckdbevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsHDF5ArrayherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| URL pointing to the full metadata file | DATABASE_URL |
| Gets the Curated Atlas metadata as a data frame. | get_metadata |
| Given a data frame of HCA metadata, returns a Seurat object corresponding to the samples in that data frame | get_seurat |
| Gets a SingleCellExperiment from curated metadata | get_single_cell_experiment |
| Gets a SingleCellExperiment from curated metadata | get_SingleCellExperiment |
| Returns unharmonised metadata for selected datasets. | get_unharmonised_dataset |
| Returns unharmonised metadata for a metadata query | get_unharmonised_metadata |
| URL pointing to the sample metadata file, which is smaller and for test, demonstration, and vignette purposes only | SAMPLE_DATABASE_URL |
