| Type: | Package |
| Title: | Spatial Transcriptomics Iterative Hierarchical Clustering |
| Version: | 0.1.0 |
| Description: | Spatial transcriptomics iterative hierarchical clustering ('stIHC'), is a method for identifying spatial gene co-expression modules, defined as groups of genes with shared spatial expression patterns. The method is applicable across spatial transcriptomics technologies with differing spatial resolution, and provides a framework for investigating the spatial organisation of gene expression in tissues. For further details, see Higgins C., Li J.J., Carey M. <doi:10.1002/qub2.70011>. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| Depends: | R (≥ 4.0.0) |
| Imports: | fdaPDE, stats, cluster, mclust |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown, covr |
| RoxygenNote: | 7.3.3 |
| Config/testthat/edition: | 3 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2026-01-08 13:37:37 UTC; crtuser |
| Author: | Catherine Higgins [aut, cre], Jingyi Jessica Li [aut], Michelle Carey [aut] |
| Maintainer: | Catherine Higgins <catherine.higgins@ucd.ie> |
| Repository: | CRAN |
| Date/Publication: | 2026-01-12 18:50:10 UTC |
Spatial Transcriptomics Iterative Hierarchical Clustering
Description
Spatial Transcriptomics Iterative Hierarchical Clustering
Usage
stIHC(data)
Arguments
data |
data frame with columns |
Value
A list with elements:
label |
Vector of cluster labels. |
mean_clusters_mat |
Matrix of cluster means. |
clusters |
List of matrices, each matrix contains the observations belonging to that cluster. |
Examples
## Load example data within the package
rds_path <- system.file("extdata", "spatial_data.rds", package = "stIHC")
example_data <- readRDS(rds_path)
## Run stIHC
stihc = stIHC(example_data)
## Inspect cluster assignments
table(stihc$label)