adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix
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 |
Documentation:
| Reference manual: | adjclust.html , adjclust.pdf |
| Vignettes: |
Clustering of Hi-C contact maps (source, R code) Implementation notes for the adjclust package (source, R code) Inferring Linkage Disequilibrium blocks from genotypes (source, R code) |
Downloads:
| Package source: | adjclust_0.6.10.tar.gz |
| Windows binaries: | r-devel: adjclust_0.6.10.zip, r-release: adjclust_0.6.10.zip, r-oldrel: adjclust_0.6.10.zip |
| macOS binaries: | r-release (arm64): adjclust_0.6.10.tgz, r-oldrel (arm64): adjclust_0.6.10.tgz, r-release (x86_64): adjclust_0.6.10.tgz, r-oldrel (x86_64): adjclust_0.6.10.tgz |
| Old sources: | adjclust archive |
Reverse dependencies:
| Reverse imports: | hicream, SISIR, treediff |
Linking:
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