Package: adjclust 0.6.11

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 Ambroise et al (2019) <doi:10.1186/s13015-019-0157-4>.

Authors:Christophe Ambroise [aut], Shubham Chaturvedi [aut], Alia Dehman [aut], Pierre Neuvial [aut, cre], Guillem Rigaill [aut], Nathalie Vialaneix [aut], Gabriel Hoffman [aut]

adjclust_0.6.11.tar.gz
adjclust_0.6.11.zip(r-4.7)adjclust_0.6.11.zip(r-4.6)adjclust_0.6.11.zip(r-4.5)
adjclust_0.6.11.tgz(r-4.6-x86_64)adjclust_0.6.11.tgz(r-4.6-arm64)adjclust_0.6.11.tgz(r-4.5-x86_64)adjclust_0.6.11.tgz(r-4.5-arm64)
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adjclust_0.6.11.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
adjclust/json (API)

# Install 'adjclust' in R:
install.packages('adjclust', repos = c('https://pneuvial.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pneuvial/adjclust/issues

Pkgdown/docs site:https://pneuvial.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

clusteringfeatureextractiongwashi-chierarchical-clusteringlinkage-disequilibriumcppopenmp

7.74 score 16 stars 3 packages 16 scripts 428 downloads 2 mentions 8 exports 30 dependencies

Last updated from:8dfea166a0. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK205
linux-devel-x86_64OK233
source / vignettesOK242
linux-release-arm64OK214
linux-release-x86_64OK240
macos-release-arm64OK183
macos-release-x86_64OK439
macos-oldrel-arm64OK222
macos-oldrel-x86_64OK477
windows-develOK174
windows-releaseOK235
windows-oldrelOK186
wasm-releaseOK177

Exports:adjClustcorrectcutree_chacdiagnosehicClustplotSimselectsnpClust

Dependencies:capusheclicpp11dendextendfarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsR6RColorBrewerRcppRcppArmadillorlangS7scalessparseMatrixStatsvctrsviridisviridisLitewithr

Clustering of Hi-C contact maps
Introduction | Loading and displaying a sample Hi-C contact map | Using hicClust | Other types of input | References | Session information
Rendered fromhicClust.Rmdusingknitr::rmarkdown

Last update: 2024-02-07
Started: 2017-10-18

Inferring Linkage Disequilibrium blocks from genotypes
Introduction | Loading and displaying genotype data | Adjacency-constrained Hierarchical Agglomerative Clustering | Output | Other types of input | References | Session information
Rendered fromsnpClust.Rmdusingknitr::rmarkdown

Last update: 2024-02-07
Started: 2017-10-18

Implementation notes for the adjclust package
Notes on relations between similarity and dissimilarity implementation | Basic implementation of CHAC in adjclust | More advanced used for kernel or similarity matrices | Non positive but normalized similarities | Non normalized similarities | Case of dissimilarity data | Options for displaying the dendrogram | mode = "corrected" | mode = "total-disp" | mode = "within-disp" | mode = "average-disp" | Relations with 'hclust' and 'rioja' | References
Rendered fromnotesCHAC.Rmdusingknitr::rmarkdown

Last update: 2022-11-08
Started: 2017-10-18

Readme and manuals

Help Manual

Help pageTopics
Adjacency-constrained ClusteringadjClust
Class chacas.hclust.chac chac correct correct.chac cutree_chac cuttree_chac diagnose diagnose.chac head.chac plot.chac print.chac summary.chac
Adjacency-constrained Clustering of Hi-C contact mapshicClust
Plot (dis)similarity matrixplotSim
Clustering selectionselect select.chac
Adjacency-constrained Clustering of Single Nucleotide PolymorphismssnpClust