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:
adjclust_0.6.10.tar.gz
adjclust_0.6.10.tar.gz(r-4.5-noble)adjclust_0.6.10.tar.gz(r-4.4-noble)
adjclust_0.6.10.tgz(r-4.4-emscripten)adjclust_0.6.10.tgz(r-4.3-emscripten)
adjclust.pdf |adjclust.html✨
adjclust/json (API)
NEWS
# Install 'adjclust' in R: |
install.packages('adjclust', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pneuvial/adjclust/issues
Pkgdown:https://pneuvial.github.io
Last updated 2 months agofrom:9604295dfd. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 08 2024 |
R-4.5-linux-x86_64 | OK | Nov 08 2024 |
Exports:adjClustcorrectcutree_chacdiagnosehicClustplotSimselectsnpClust
Dependencies:capusheclicolorspacedendextendfansifarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppArmadillorlangscalessparseMatrixStatstibbleutf8vctrsviridisviridisLitewithr
Clustering of Hi-C contact maps
Rendered fromhicClust.Rmd
usingknitr::rmarkdown
on Nov 08 2024.Last update: 2024-02-09
Started: 2017-10-18
Implementation notes for the adjclust package
Rendered fromnotesCHAC.Rmd
usingknitr::rmarkdown
on Nov 08 2024.Last update: 2023-04-27
Started: 2017-10-18
Inferring Linkage Disequilibrium blocks from genotypes
Rendered fromsnpClust.Rmd
usingknitr::rmarkdown
on Nov 08 2024.Last update: 2024-02-09
Started: 2017-10-18
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Adjacency-constrained Clustering | adjClust |
Class chac | as.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 maps | hicClust |
Plot (dis)similarity matrix | plotSim |
Clustering selection | select select.chac |
Adjacency-constrained Clustering of Single Nucleotide Polymorphisms | snpClust |