CRAN/E | adjclust

adjclust

Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix

Installation

About

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.

Citation adjclust citation info
pneuvial.github.io/adjclust/
Bug report File report

Key Metrics

Version 0.6.9
R ≥ 4.0.0
Published 2024-02-08 50 days ago
Needs compilation? yes
License GPL-3
CRAN checks adjclust results
Language en-US

Downloads

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Maintainer

Maintainer

Pierre Neuvial

pierre.neuvial@math.univ-toulouse.fr

Authors

Christophe Ambroise

aut

Shubham Chaturvedi

aut

Alia Dehman

aut

Pierre Neuvial

aut / cre

Guillem Rigaill

aut

Nathalie Vialaneix

aut

Gabriel Hoffman

aut

Material

README
NEWS
Reference manual
Package source

In Views

Omics

Vignettes

Clustering of Hi-C contact maps
Implementation notes for the adjclust package
Inferring Linkage Disequilibrium blocks from genotypes

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

adjclust archive

Depends

R ≥ 4.0.0

Imports

stats
graphics
grDevices
Rcpp ≥ 1.0.6
Matrix
sparseMatrixStats
methods
utils
capushe
ggplot2
dendextend
rlang

Suggests

knitr
testthat
rmarkdown
rioja
HiTC
snpStats
BiocGenerics

LinkingTo

Rcpp
RcppArmadillo

Reverse Imports

SISIR
treediff