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This vignette provides an introduction to the R package
DR.SC, where the function DR.SC implements the
model DR-SC, spatial clustering with hidden Markov random
field using empirical Bayes. The package can be installed with the
following command from Github:
install.packages('remotes')
remotes::install_github("feiyoung/DR.SC")
or install from CRAN
install.packages("DR.SC")
The package can be loaded with the command:
library("DR.SC")
#> Loading required package: parallel
#> Loading required package: spatstat.geom
#> Loading required package: spatstat.data
#> Loading required package: spatstat.univar
#> spatstat.univar 3.0-1
#> spatstat.geom 3.3-3
#> DR.SC : Joint dimension reduction and spatial clustering is conducted for
#> Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
#> Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well. Check out our Package website (https://feiyoung.github.io/DR.SC/index.html) for a more complete description of the methods and analysesFor running big data, users can use the following system command to
set the C_stack unlimited in case of
R Error: C stack usage is too close to the limit.
ulimit -s unlimitedThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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