Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix [R package adjclust version 0.6.10]

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年10月08日

DOI: 10.32614/CRAN.package.adjclust

Author: Christophe Ambroise [aut], Shubham Chaturvedi [aut], Alia Dehman [aut], Pierre Neuvial ORCID iD [aut, cre], Guillem Rigaill [aut], Nathalie Vialaneix ORCID iD [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 [issues need fixing before 2025年12月05日]