adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix (original) (raw)
Implements a constrained version of hierarchical agglomerative clustering, in which each observation is associated to a position, and only adjacent clusters can be merged. Typical application fields in bioinformatics include Genome-Wide Association Studies or Hi-C data analysis, where the similarity between items is a decreasing function of their genomic distance. Taking advantage of this feature, the implemented algorithm is time and memory efficient. This algorithm is described in Ambroise et al (2019) <doi:10.1186/s13015-019-0157-4>.
| Version: | 0.6.10 |
|---|---|
| Depends: | R (≥ 4.0.0) |
| Imports: | stats, graphics, grDevices, Rcpp (≥ 1.0.6), Matrix, sparseMatrixStats, methods, utils, capushe, ggplot2, dendextend, rlang |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | knitr, testthat, rmarkdown, rioja, HiTC, snpStats, BiocGenerics |
| Published: | 2024-10-08 |
| DOI: | 10.32614/CRAN.package.adjclust |
| Author: | Christophe Ambroise [aut], Shubham Chaturvedi [aut], Alia Dehman [aut], Pierre Neuvial  [aut, cre], Guillem Rigaill [aut], Nathalie Vialaneix [aut], Gabriel Hoffman [aut] |
| Maintainer: | Pierre Neuvial <pierre.neuvial at math.univ-toulouse.fr> |
| BugReports: | https://github.com/pneuvial/adjclust/issues |
| License: | GPL-3 |
| URL: | https://pneuvial.github.io/adjclust/ |
| NeedsCompilation: | yes |
| Language: | en-US |
| Citation: | adjclust citation info |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | adjclust results |
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