R: Hidden Markov Random Field for Spatial Transcriptomic Data

# Hidden Markov Random Field for Spatial Transcriptomic Data

## Documentation for package ‘smfishHmrf’ version 0.1

- DESCRIPTION file
- Package README

## Help Pages

findDampFactor | findDampFactor
seqfishplus | SeqFISHplus dataset
smfishHmrf | smfishHmrf: A package for running hidden markov random field on smFISH and other spatial transcriptomic datasets
smfishHmrf.generate.centroid | Generate cluster centroids, where input is given as a matrix.
smfishHmrf.generate.centroid.it | Generate cluster centroids, where input is a file.
smfishHmrf.generate.centroid.save | Save the cluster centroids to file
smfishHmrf.generate.centroid.use.exist | Use existing cluster centroids
smfishHmrf.hmrfem.multi | Performs HMRF for multivariate normal distribution. Accepts R data structures as inputs. Accepts a single beta.
smfishHmrf.hmrfem.multi.it | Perform HMRF for multivariate normal distribution. Accepts R data structures as inputs. Accepts multiple betas.
smfishHmrf.hmrfem.multi.it.min | Perform HMRF on multivariate normal distributions. Accepts file names as inputs. Accepts multiple betas.
smfishHmrf.hmrfem.multi.save | Save the HMRF result
smfishHmrf.read.expression | smfishHmrf.read.expression