Hidden Markov Random Field for Spatial Transcriptomic Data
checkErrors
checkErrorsMulti
checkStopVerbose
checkStopVerboseMulti
findDampFactor
getDen
initialIndices
initialIndicesMulti
relerr.multi
relerr
Generate cluster centroids, where input is a file.
Generate cluster centroids, where input is given as a matrix.
Save the cluster centroids to file
Use existing cluster centroids
Perform HMRF on multivariate normal distributions. Accepts file names ...
Perform HMRF for multivariate normal distribution. Accepts R data stru...
Performs HMRF for multivariate normal distribution. Accepts R data str...
Save the HMRF result
smfishHmrf.hmrfem
smfishHmrf: A package for running hidden markov random field on smFISH...
smfishHmrf.read.expression
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>.
Useful links