Package: coca 1.1.0

Alessandra Cabassi

coca: Cluster-of-Clusters Analysis

Contains the R functions needed to perform Cluster-Of-Clusters Analysis (COCA) and Consensus Clustering (CC). For further details please see Cabassi and Kirk (2020) <doi:10.1093/bioinformatics/btaa593>.

Authors:Alessandra Cabassi [aut, cre], Paul DW Kirk [ths]

coca_1.1.0.tar.gz
coca_1.1.0.zip(r-4.5)coca_1.1.0.zip(r-4.4)coca_1.1.0.zip(r-4.3)
coca_1.1.0.tgz(r-4.5-any)coca_1.1.0.tgz(r-4.4-any)coca_1.1.0.tgz(r-4.3-any)
coca_1.1.0.tar.gz(r-4.5-noble)coca_1.1.0.tar.gz(r-4.4-noble)
coca_1.1.0.tgz(r-4.4-emscripten)coca_1.1.0.tgz(r-4.3-emscripten)
coca.pdf |coca.html✨
coca/json (API)

# Install 'coca' in R:

install.packages('coca', repos = c('https://acabassi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/acabassi/coca/issues

On CRAN:

cluster-analysis cluster-of-clusters clustering coca genomics integrative-clustering multi-omics

5.03 score 6 stars 1 packages 12 scripts 215 downloads 1 mentions 8 exports 90 dependencies

Last updated 5 years agofrom:b89ca330ed. Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 11 2025
R-4.5-win	NOTE	Feb 11 2025
R-4.5-mac	NOTE	Feb 11 2025
R-4.5-linux	NOTE	Feb 11 2025
R-4.4-win	NOTE	Feb 11 2025
R-4.4-mac	NOTE	Feb 11 2025
R-4.3-win	NOTE	Feb 11 2025
R-4.3-mac	NOTE	Feb 11 2025

Exports:buildMOC chooseKusingAUC coca consensusCluster expandMOC fillMOC maximiseSilhouette plotMOC

Dependencies:caret class cli clock cluster codetools colorspace cpp11 data.table DEoptimR diagram digest diptest dplyr e1071 fansi farver flexmix foreach fpc future future.apply generics ggplot2 glmnet globals glue gower gtable hardhat ipred isoband iterators kernlab KernSmooth labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix mclust mgcv ModelMetrics modeltools munsell nlme nnet numDeriv parallelly pheatmap pillar pkgconfig plyr prabclus pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp RcppEigen recipes reshape2 rlang robustbase rpart scales shape sparcl sparsevctrs SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr

Introduction to coca

Alessandra Cabassi

Rendered fromcoca-vignette.Rmdusingknitr::rmarkdownon Feb 11 2025.

Last update: 2020-07-08
Started: 2018-10-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build Matrix-Of-Clusters	buildMOC
Choose number of clusters based on AUC	chooseKusingAUC
Cluster-Of-Clusters Analysis	coca
Consensus clustering	consensusCluster
Expand matrix of clusters	expandMOC
Fill Matrix-Of-Clusters	fillMOC
Choose K that maximises the silhouette from a set of kernel matrices and clusterings	maximiseSilhouette
Plot Matrix-Of-Clusters	plotMOC