bioc-issue-bot
commented
2 weeks ago Hi @lchengy1024
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The DESCRIPTION file for this package is:
Package: SpatialDeX
Type: Package
Title: What the Package Does (Title Case)
Version: 0.99.0
Authors@R: c(
person("Xinyi", "Liu", email = "Xinyiliu@uic.edu",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-5716-8264")))
Maintainer: Xinyi Liu <xinyiliu@uic.edu>
Description: The rapid development of spatial transcriptomics (ST) technologies has
enabled transcriptome-wide profiling of gene expression in tissue sections.
Despite the emergence of single-cell resolution platforms, most ST
sequencing studies still operate at the multi-cell resolution. Consequently,
deconvolution of cell identities within the spatial spots has become
imperative for characterizing cell type-specific spatial organization.
To this end, we introduce SpatialDeX, a regression model-based method for
estimating cell type proportions in tumor ST spots. SpatialDeX exhibited
comparable performance to reference-based methods and outperformed other
reference-free methods with simulated ST data. Using experimental ST data,
SpatialDeX demonstrated superior performance compared with both
reference-based and reference-free approaches.
License: GPL-2
Encoding: UTF-8
LazyData: false
Imports:
dplyr,
GSVA,
copykat
RoxygenNote: 7.3.1
Data: extdata/cyclegenes.RData extdata/DNA.hg20.RData extdata/full.anno.RData
biocViews: Spatial, Transcriptomics, Software
URL: https://github.com/wang-lab/SpatialDeX/
BugReports: https://github.com/wang-lab/SpatialDeX/issues
VignetteEngine: knitr::rmarkdown
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
Depends:
R (>= 2.10)
vjcitn
lshep
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