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>.

Version: 0.5.2
Depends: R (≥ 2.10.0)
Imports: Matrix, matrixStats, snpStats, methods, utils, HiTC
Suggests: BiocStyle, knitr, testthat, rmarkdown, rioja
Published: 2017-10-18
Author: Christophe Ambroise [aut], Shubham Chaturvedi [aut], Alia Dehman [aut], Michel Koskas [aut], Pierre Neuvial [aut, cre], Guillem Rigaill [aut], Nathalie Villa-Vialaneix [aut]
Maintainer: Pierre Neuvial <pierre.neuvial at math.univ-toulouse.fr>
BugReports: https://github.com/pneuvial/adjclust/issues
License: GPL-3
URL: https://github.com/pneuvial/adjclust
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: adjclust results

Downloads:

Reference manual: adjclust.pdf
Vignettes: Clustering of Hi-C contact maps
Notes on CHAC implementation in adjclust
Inferring Linkage Disequilibrium blocks from genotypes
Package source: adjclust_0.5.2.tar.gz
Windows binaries: r-devel: adjclust_0.5.2.zip, r-release: adjclust_0.5.2.zip, r-oldrel: adjclust_0.5.2.zip
OS X El Capitan binaries: r-release: not available
OS X Mavericks binaries: r-oldrel: adjclust_0.5.2.tgz

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