Package: Azimuth 0.5.0

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:Andrew Butler [aut], Charlotte Darby [aut], Yuhan Hao [aut], Austin Hartman [aut], Paul Hoffman [aut, cre], Jaison Jain [ctb], Gesmira Molla [aut], Rahul Satija [aut], Satija Lab and Collaborators [fnd]

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'))

Peer review:

Bug tracker:https://github.com/satijalab/azimuth/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

shiny-appsingle-cell-genomicssingle-cell-rna-seq

19 exports 100 stars 4.20 score 240 dependencies

Last updated 8 months agofrom:243ee5db80

Exports:AzimuthAppAzimuthBridgeReferenceAzimuthReferenceConnectConvertGeneNamesCreateAzimuthDataCreateColorMapGetColorMapGetPlotRefLoadBridgeReferenceLoadFileInputLoadH5ADobsLoadReferenceReferenceVersionRunAzimuthRunAzimuthATACSaveAzimuthReferenceSetColorMapValidateAzimuthReference

Dependencies:abindannotateAnnotationDbiAnnotationFilteraskpassbase64encbeachmatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg38bslibcachemcaToolscellrangerclicliprclusterCNErcodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDelayedMatrixStatsdeldirdigestDirichletMultinomialdotCall64dplyrdqrngDTEnsDb.Hsapiens.v86ensembldbevaluatefansifarverfastDummiesfastmapfastmatchfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygarglegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelggridgesglmGamPoiglobalsglueGO.dbgoftestgoogledrivegooglesheets4gplotsgridExtragtablegtoolsHDF5Arrayhdf5rherehighrhmshtmltoolshtmlwidgetshttpuvhttricaidsigraphIRangesirlbaisobandJASPAR2020jquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplogrplotlyplyrpngpolyclippoweRlawpracmaprestoprettyunitsprogressprogressrpromisesProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppRollRcppTOMLRCurlreadrrematchrematch2reshape2restfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownROCRrprojrootRsamtoolsRSpectraRSQLitertracklayerRtsneS4ArraysS4VectorssassscalesscattermoresctransformseqLogoSeuratSeuratDataSeuratDiskSeuratObjectshinyshinyBSshinydashboardshinyjsSignacSingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrSummarizedExperimentsurvivalsystensorTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8uuiduwotvctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell DataAzimuth-package Azimuth
Launch the mapping appAzimuthApp
Create a Seurat object compatible with Azimuth.AzimuthBridgeReference
AzimuthDataAzimuthData AzimuthData-class
Create a Seurat object compatible with Azimuth.AzimuthReference
Converts gene names of query to match type/species of reference names (human or mouse).ConvertGeneNames
Create an 'AzimuthData' objectCreateAzimuthData
Create A Color MapCreateColorMap
Get Azimuth color mappingGetColorMap GetColorMap.AzimuthData GetColorMap.Seurat
Get Azimuth plotrefGetPlotRef GetPlotRef.AzimuthData GetPlotRef.Seurat
Get transcripts modified from Signac::GeneActivityGetTranscripts
Load the extended reference RDS file for bridge integrationLoadBridgeReference
Load file input into a 'Seurat' objectLoadFileInput
Load obs from a H5AD fileLoadH5ADobs
Load the reference RDS filesLoadReference
Get Azimuth reference version numberReferenceVersion ReferenceVersion.AzimuthData ReferenceVersion.Seurat
Run Azimuth annotationRunAzimuth RunAzimuth.character RunAzimuth.Seurat
Run Azimuth annotation for ATAC queryRunAzimuthATAC RunAzimuthATAC.character RunAzimuthATAC.Seurat
Save 'Azimuth' references and neighbors index to same folderSaveAzimuthReference
Set Azimuth color mappingSetColorMap SetColorMap.AzimuthData SetColorMap.Seurat
Validate References for AzimuthValidateAzimuthReference