Hidden Markov Random Field for Spatial Transcriptomic Data
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Documentation for package ‘smfishHmrf’ version 0.1
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 |