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: | 0.5.6 |
Depends: | R (≥ 2.10.0) |
Imports: | Matrix, matrixStats, methods, utils |
Suggests: | knitr, testthat, rmarkdown, rioja, HiTC, snpStats |
Published: | 2018-02-08 |
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 |
Reference manual: | adjclust.pdf |
Vignettes: |
Clustering of Hi-C contact maps Implementation notes for the adjclust package Inferring Linkage Disequilibrium blocks from genotypes |
Package source: | adjclust_0.5.6.tar.gz |
Windows binaries: | r-devel: adjclust_0.5.6.zip, r-release: adjclust_0.5.6.zip, r-oldrel: adjclust_0.5.6.zip |
OS X El Capitan binaries: | r-release: adjclust_0.5.6.tgz |
OS X Mavericks binaries: | r-oldrel: adjclust_0.5.2.tgz |
Old sources: | adjclust archive |
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