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DESCRIPTION
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Package: Voyager
Type: Package
Title: From geospatial to spatial omics
Version: 1.8.1
Authors@R:
c(person("Lambda", "Moses", email = "[email protected]",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7092-9427")),
person("Alik", "Huseynov",
comment = c(ORCID = "0000-0002-1438-4389"),
role = "aut"),
person("Kayla", "Jackson", email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0001-6483-0108")),
person("Laura", "Luebbert", email = "[email protected]",
role = c("aut"),
comment = c(ORCID = "0000-0003-1379-2927")),
person("Lior", "Pachter", email = "[email protected]",
role = c("aut", "rev"),
comment = c(ORCID = "0000-0002-9164-6231")))
Description: SpatialFeatureExperiment (SFE) is a new S4 class for working with
spatial single-cell genomics data. The voyager package implements basic
exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods
include univariate global spatial ESDA methods such as Moran's I,
permutation testing for Moran's I, and correlograms. Bivariate methods
include Lee's L and cross variogram. Multivariate methods include MULTISPATI
PCA and multivariate local Geary's C recently developed by Anselin. The
Voyager package also implements plotting functions to plot SFE data and ESDA
results.
Depends:
R (>= 4.2.0),
SpatialFeatureExperiment (>= 1.7.3)
Imports:
BiocParallel,
bluster,
DelayedArray,
ggnewscale,
ggplot2 (>= 3.4.0),
grDevices,
grid,
lifecycle,
Matrix,
matrixStats,
memuse,
methods,
patchwork,
rlang,
RSpectra,
S4Vectors,
scales,
scico,
sf,
SingleCellExperiment,
SpatialExperiment,
spdep,
stats,
SummarizedExperiment,
terra,
utils,
zeallot
Suggests:
arrow,
automap,
BiocSingular,
BiocStyle,
cowplot,
data.table,
EBImage,
ExperimentHub,
ggh4x,
gstat,
hexbin,
knitr,
pheatmap,
RBioFormats,
rhdf5,
rmarkdown,
scater,
scattermore,
scran,
sfarrow,
SFEData,
testthat (>= 3.0.0),
vdiffr,
xml2
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.3.2
Config/testthat/edition: 3
biocViews:
GeneExpression,
Spatial,
Transcriptomics,
Visualization
VignetteBuilder: knitr
URL: https://github.com/pachterlab/voyager
BugReports: https://github.com/pachterlab/voyager/issues
Collate:
'AllGenerics.R'
'res2df.R'
'SFEMethod-class.R'
'SFEMethod-bivariate.R'
'SFEMethod-multivariate.R'
'SFEMethod-spdep.R'
'bivariate.R'
'data.R'
'featureData.R'
'geom_spi.R'
'gstat.R'
'listSFEMethods.R'
'multivariate.R'
'plot-non-spatial.R'
'plot-transcripts.R'
'plot-univar-downstream.R'
'plot.R'
'plotLocalResult.R'
'plotSpatialReducedDim.R'
'spatial-misc.R'
'univariate-downstream.R'
'univariate-internal.R'
'univariate.R'
'utils.R'