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) <https://almob.biomedcentral.com/articles/10.1186/s13015-019-0157-4>.
| Version: | 0.6.6 |
| Depends: | R (≥ 4.0.0) |
| Imports: | stats, graphics, grDevices, Rcpp (≥ 1.0.6), Matrix, sparseMatrixStats, methods, utils, capushe |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | knitr, testthat, rmarkdown, rioja, HiTC, snpStats, BiocGenerics |
| Published: | 2022-09-14 |
| 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 |
| CRAN checks: | adjclust results |
| Reference manual: | adjclust.pdf |
| Vignettes: |
Clustering of Hi-C contact maps Implementation notes for the adjclust package Inferring Linkage Disequilibrium blocks from genotypes |
| Package source: | adjclust_0.6.6.tar.gz |
| Windows binaries: | r-devel: adjclust_0.6.6.zip, r-release: adjclust_0.6.6.zip, r-oldrel: adjclust_0.6.6.zip |
| macOS binaries: | r-release (arm64): adjclust_0.6.6.tgz, r-oldrel (arm64): adjclust_0.6.6.tgz, r-release (x86_64): adjclust_0.6.6.tgz, r-oldrel (x86_64): adjclust_0.6.6.tgz |
| Old sources: | adjclust archive |
| Reverse imports: | SISIR |
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