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smfishHmrf
View on CRAN: Click
here
Download and install smfishHmrf package within the R console
Install from CRAN:
install.packages("smfishHmrf")
Install from Github:
library("remotes")
install_github("cran/smfishHmrf") Install by package version:
library("remotes")
install_version("smfishHmrf", "0.1") Attach the package and use:
library("smfishHmrf")
Maintained by
Qian Zhu
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-11-03
Latest Update: 2020-11-03
Description:
Discovery of spatial patterns with Hidden Markov Random Field. This package is designed for spatial transcriptomic data and single molecule fluorescent in situ hybridization (FISH) data such as sequential fluorescence in situ hybridization (seqFISH) and multiplexed error-robust fluorescence in situ hybridization (MERFISH). The methods implemented in this package are described in Zhu et al. (2018) <doi:10.1038/nbt.4260>.
How to cite:
Qian Zhu (2020). smfishHmrf: Hidden Markov Random Field for Spatial Transcriptomic Data. R package version 0.1, https://cran.r-project.org/web/packages/smfishHmrf. Accessed 22 Sep. 2026.
Previous versions and publish date:
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Complete documentation for smfishHmrf
Functions, R codes and Examples using
the smfishHmrf R package
Some associated functions: checkErrors . checkErrorsMulti . checkStopVerbose . checkStopVerboseMulti . findDampFactor . getDen . initialIndices . initialIndicesMulti . relerr.multi . relerr . seqfishplus . smfishHmrf.generate.centroid.it . smfishHmrf.generate.centroid . smfishHmrf.generate.centroid.save . smfishHmrf.generate.centroid.use.exist . smfishHmrf.hmrfem.multi.it.min . smfishHmrf.hmrfem.multi.it . smfishHmrf.hmrfem.multi . smfishHmrf.hmrfem.multi.save . smfishHmrf.hmrfem . smfishHmrf . smfishHmrf.read.expression .
Some associated R codes: common.R . seqfishplus.R . smfishHmrf.R . smfishHmrf.hmrfem.R . update.R . Full smfishHmrf package functions and examples
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