Package: adjclust 0.6.10

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]

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adjclust.pdf |adjclust.html
adjclust/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

clusteringfeatureextractiongwashi-chierarchical-clusteringlinkage-disequilibrium

7.75 score 16 stars 2 packages 13 scripts 634 downloads 2 mentions 8 exports 37 dependencies

Last updated 2 months agofrom:d2e0b903fd. Checks:OK: 8 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-win-x86_64OKNov 06 2024
R-4.5-linux-x86_64OKNov 06 2024
R-4.4-win-x86_64OKNov 06 2024
R-4.4-mac-x86_64OKNov 06 2024
R-4.4-mac-aarch64OKNov 06 2024
R-4.3-win-x86_64OKNov 06 2024
R-4.3-mac-x86_64OKNov 06 2024
R-4.3-mac-aarch64NOTENov 06 2024

Exports:adjClustcorrectcutree_chacdiagnosehicClustplotSimselectsnpClust

Dependencies:capusheclicolorspacedendextendfansifarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppArmadillorlangscalessparseMatrixStatstibbleutf8vctrsviridisviridisLitewithr

Clustering of Hi-C contact maps

Rendered fromhicClust.Rmdusingknitr::rmarkdownon Nov 06 2024.

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

Implementation notes for the adjclust package

Rendered fromnotesCHAC.Rmdusingknitr::rmarkdownon Nov 06 2024.

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

Inferring Linkage Disequilibrium blocks from genotypes

Rendered fromsnpClust.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-02-07
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