adjclust

swMATH28002CRANadjclustMaRDI QIDQ39716

Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix

Guillem Rigaill, Pierre Neuvial, Shubham Chaturvedi, Alia Dehman, Gabriel Hoffman, Christophe Ambroise, Nathalie Vialaneix

Last update: 8 February 2024

Copyright license: GNU General Public License, version 3.0

Software version identifier: 0.6.6, 0.6.7, 0.5.2, 0.5.6, 0.5.7, 0.5.9, 0.5.99, 0.6.3, 0.6.4, 0.6.5, 0.6.6, 0.6.8, 0.6.9

Source code repository: https://github.com/cran/adjclust

Description

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>.

Cites work

• Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics

Related Items (3)

Applicability and interpretability of Ward's hierarchical agglomerative clustering with or without contiguity constraints ⋮ treediff ⋮ SISIR

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