bioc-issue-bot
commented
2 months ago Hi @Nick-Eagles
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: visiumStitched
Title: Enable downstream analysis of Visium capture areas stitched together with
Fiji
Version: 0.99.0
Date: 2024-07-19
Authors@R:
c(
person("Nicholas J.", "Eagles", email = "nickeagles77@gmail.com",
role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9808-5254")),
person("Leonardo", "Collado-Torres", role = c("ctb"),
email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X"))
)
Description: This package provides helper functions for working with
multiple Visium capture areas that overlap each other. This package was
developed along with the companion example use case data available from
https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched
prepares SpaceRanger (10x Genomics) output files so you can stitch the
images from groups of capture areas together with Fiji. Then visiumStitched
builds a SpatialExperiment object with the stitched data and makes an
artificial hexogonal grid enabling the seamless use of spatial clustering
methods that rely on such grid to identify neighboring spots, such as
PRECAST and BayesSpace. The SpatialExperiment objects created by
visiumStitched are compatible with spatialLIBD, which can be used to build
interactive websites for stitched SpatialExperiment objects. visiumStitched
also enables casting SpatialExperiment objects as Seurat objects.
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
R (>= 4.4),
SpatialExperiment
Suggests:
BiocFileCache,
BiocStyle,
ggplot2,
knitr,
RefManageR,
rmarkdown,
sessioninfo,
testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Imports:
dplyr,
DropletUtils,
grDevices,
imager,
pkgcond,
readr,
rjson,
S4Vectors,
Seurat,
spatialLIBD,
stringr,
SummarizedExperiment,
xml2
biocViews: Software, Spatial, Transcriptomics, Transcription, GeneExpression,
Visualization, DataImport
URL: https://github.com/LieberInstitute/visiumStitched
BugReports: https://support.bioconductor.org/tag/visiumStitched
LazyData: true
lcolladotor
lshep
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