Package: Azimuth 0.5.0
![](https://r-universe.dev/static/nobody.jpg)
Paul Hoffman
Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data
Azimuth uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery).
Authors:
Azimuth_0.5.0.tar.gz
Azimuth_0.5.0.tar.gz(r-4.4-noble)
Azimuth.pdf |Azimuth.html✨
Azimuth/json (API)
NEWS
# Install 'Azimuth' in R: |
install.packages('Azimuth', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/satijalab/azimuth/issues
shiny-appsingle-cell-genomicssingle-cell-rna-seq
Last updated 10 months agofrom:243ee5db80. Checks:OK: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 14 2024 |
Exports:AzimuthAppAzimuthBridgeReferenceAzimuthReferenceConnectConvertGeneNamesCreateAzimuthDataCreateColorMapGetColorMapGetPlotRefLoadBridgeReferenceLoadFileInputLoadH5ADobsLoadReferenceReferenceVersionRunAzimuthRunAzimuthATACSaveAzimuthReferenceSetColorMapValidateAzimuthReference
Dependencies:abindannotateAnnotationDbiAnnotationFilteraskpassbase64encbeachmatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg38bslibcachemcaToolscellrangerclicliprclusterCNErcodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDelayedMatrixStatsdeldirdigestDirichletMultinomialdotCall64dplyrdqrngDTEnsDb.Hsapiens.v86ensembldbevaluatefansifarverfastDummiesfastmapfastmatchfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygarglegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelggridgesglmGamPoiglobalsglueGO.dbgoftestgoogledrivegooglesheets4gplotsgridExtragtablegtoolsHDF5Arrayhdf5rherehighrhmshtmltoolshtmlwidgetshttpuvhttricaidsigraphIRangesirlbaisobandJASPAR2020jquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplogrplotlyplyrpngpolyclippoweRlawpracmaprestoprettyunitsprogressprogressrpromisesProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppRollRcppTOMLRCurlreadrrematchrematch2reshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownROCRrprojrootRsamtoolsRSpectraRSQLitertracklayerRtsneS4ArraysS4VectorssassscalesscattermoresctransformseqLogoSeuratSeuratDataSeuratDiskSeuratObjectshinyshinyBSshinydashboardshinyjsSignacSingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensorTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8uuiduwotvctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioczoo