R package 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 Chapter 4 of Alia Dehman (2015) <https://hal.archives-ouvertes.fr/tel-01288568v1>.
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References in zbMATH (referenced in 1 article , 1 standard article )
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- Christophe Ambroise, Alia Dehman, Pierre Neuvial, Guillem Rigaill, Nathalie Vialaneix: Adjacency-constrained hierarchical clustering of a band similarity matrix with application to Genomics (2019) arXiv