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'))

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

shiny-app single-cell-genomics single-cell-rna-seq

19 exports 103 stars 4.25 score 241 dependencies 223 scripts

Last updated 10 months agofrom:243ee5db80. Checks:OK: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 14 2024

Exports:AzimuthApp AzimuthBridgeReference AzimuthReference Connect ConvertGeneNames CreateAzimuthData CreateColorMap GetColorMap GetPlotRef LoadBridgeReference LoadFileInput LoadH5ADobs LoadReference ReferenceVersion RunAzimuth RunAzimuthATAC SaveAzimuthReference SetColorMap ValidateAzimuthReference

Dependencies:abind annotate AnnotationDbi AnnotationFilter askpass base64enc beachmat BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg38 bslib cachem caTools cellranger cli clipr cluster CNEr codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray DelayedMatrixStats deldir digest DirichletMultinomial dotCall64 dplyr dqrng DT EnsDb.Hsapiens.v86 ensembldb evaluate fansi farver fastDummies fastmap fastmatch fitdistrplus FNN fontawesome formatR fs futile.logger futile.options future future.apply gargle generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel ggridges glmGamPoi globals glue GO.db goftest googledrive googlesheets4 gplots gridExtra gtable gtools HDF5Array hdf5r here highr hms htmltools htmlwidgets httpuv httr ica ids igraph IRanges irlba isoband JASPAR2020 jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leiden lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plogr plotly plyr png polyclip poweRlaw pracma presto prettyunits progress progressr promises ProtGenerics purrr pwalign R.methodsS3 R.oo R.utils R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppRoll RcppTOML RCurl readr rematch rematch2 reshape2 restfulr reticulate rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown ROCR rprojroot Rsamtools RSpectra RSQLite rtracklayer Rtsne S4Arrays S4Vectors sass scales scattermore sctransform seqLogo Seurat SeuratData SeuratDisk SeuratObject shiny shinyBS shinydashboard shinyjs Signac SingleCellExperiment sitmo snow sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 uuid uwot vctrs viridisLite vroom withr xfun XML xtable XVector yaml zlibbioc zoo

Help page	Topics
Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data	Azimuth-package Azimuth
Launch the mapping app	AzimuthApp
Create a Seurat object compatible with Azimuth.	AzimuthBridgeReference
AzimuthData	AzimuthData 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' object	CreateAzimuthData
Create A Color Map	CreateColorMap
Get Azimuth color mapping	GetColorMap GetColorMap.AzimuthData GetColorMap.Seurat
Get Azimuth plotref	GetPlotRef GetPlotRef.AzimuthData GetPlotRef.Seurat
Get transcripts modified from Signac::GeneActivity	GetTranscripts
Load the extended reference RDS file for bridge integration	LoadBridgeReference
Load file input into a 'Seurat' object	LoadFileInput
Load obs from a H5AD file	LoadH5ADobs
Load the reference RDS files	LoadReference
Get Azimuth reference version number	ReferenceVersion ReferenceVersion.AzimuthData ReferenceVersion.Seurat
Run Azimuth annotation	RunAzimuth RunAzimuth.character RunAzimuth.Seurat
Run Azimuth annotation for ATAC query	RunAzimuthATAC RunAzimuthATAC.character RunAzimuthATAC.Seurat
Save 'Azimuth' references and neighbors index to same folder	SaveAzimuthReference
Set Azimuth color mapping	SetColorMap SetColorMap.AzimuthData SetColorMap.Seurat
Validate References for Azimuth	ValidateAzimuthReference

Package: Azimuth 0.5.0

Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data

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