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DESCRIPTION
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DESCRIPTION
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Package: Azimuth
Type: Package
Title: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data
Version: 0.5.0
Date: 2023-04-06
Authors@R: c(
person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
person(given = "Charlotte", family = "Darby", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0003-2195-5300")),
person(given = "Yuhan", family = "Hao", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-1810-0822")),
person(given = "Austin", family = "Hartman", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-7278-1852')),
person(given = "Paul", family = "Hoffman", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
person(given = "Jaison", family = "Jain", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-8628-5056')),
person(given = "Rahul", family = "Satija", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-9448-8833")),
person("Satija Lab and Collaborators", role = "fnd")
)
Description: 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).
URL: https://github.com/satijalab/azimuth
BugReports: https://github.com/satijalab/azimuth/issues
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
biocViews:
Remotes:
immunogenomics/presto,
satijalab/seurat-data,
mojaveazure/seurat-disk
Depends:
R (>= 4.0.0)
Imports:
BSgenome.Hsapiens.UCSC.hg38,
DT (>= 0.15),
EnsDb.Hsapiens.v86,
future (>= 1.19.1),
ggplot2 (>= 3.3.2),
glmGamPoi (>= 1.0.0),
googlesheets4 (>= 0.2.0),
hdf5r (>= 1.3.2),
htmltools (>= 0.5.0),
httr (>= 1.4.2),
JASPAR2020,
jsonlite (>= 1.7.0),
Matrix (>= 1.2.18),
methods,
patchwork (>= 1.0.1),
presto,
Rcpp (>= 1.0.7),
rlang (>= 0.4.8),
scales (>= 1.1.1),
Seurat (>= 5.0.0),
SeuratDisk,
SeuratObject (>= 5.0.0),
SeuratData,
shiny (>= 1.5.0),
shinyBS (>= 0.61),
shinydashboard (>= 0.7.1),
shinyjs (>= 2.0.0),
Signac (>= 1.12.0),
stats,
stringr (>= 1.4.0),
TFBSTools,
tools,
utils,
plotly,
withr (>= 2.3.0)
LinkingTo: Rcpp(>= 0.11.0)
Collate:
'RcppExports.R'
'zzz.R'
'ui.R'
'helpers.R'
'azimuth.R'
'generics.R'
'server.R'