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 |
Reference manual: | 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) |
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 imports: | SISIR, treediff |
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