Package: CuratedAtlasQueryR 1.5.0

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: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]

CuratedAtlasQueryR_1.5.0.tar.gz
CuratedAtlasQueryR_1.5.0.zip(r-4.5)CuratedAtlasQueryR_1.5.0.zip(r-4.4)CuratedAtlasQueryR_1.5.0.zip(r-4.3)
CuratedAtlasQueryR_1.5.0.tgz(r-4.4-any)CuratedAtlasQueryR_1.5.0.tgz(r-4.3-any)
CuratedAtlasQueryR_1.5.0.tar.gz(r-4.5-noble)CuratedAtlasQueryR_1.5.0.tar.gz(r-4.4-noble)
CuratedAtlasQueryR_1.5.0.tgz(r-4.4-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'))

Peer review:

Bug tracker:https://github.com/stemangiola/curatedatlasqueryr/issues

On BioConductor:CuratedAtlasQueryR-1.3.0(bioc 3.21)CuratedAtlasQueryR-1.4.0(bioc 3.20)

assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsdatabaseduckdbhdf5human-cell-atlassingle-cellsinglecellexperimenttidyverse

6.17 score 89 stars 37 scripts 128 downloads 7 exports 171 dependencies

Last updated 23 days agofrom:7febec38b9. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 14 2024
R-4.5-winWARNINGNov 14 2024
R-4.5-linuxWARNINGNov 14 2024
R-4.4-winWARNINGNov 14 2024
R-4.4-macWARNINGNov 14 2024
R-4.3-winWARNINGNov 14 2024
R-4.3-macWARNINGNov 14 2024

Exports:DATABASE_URLget_metadataget_seuratget_single_cell_experimentget_SingleCellExperimentget_unharmonised_metadataSAMPLE_DATABASE_URL

Dependencies:abindaskpassassertthatbase64encBHBiobaseBiocGenericsbitopsblobbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydeldirdigestdotCall64dplyrdqrngduckdbevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsHDF5ArrayherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo