Package: cola
Type: Package
Title: A Framework for Consensus Partitioning
Version: 2.16.0
Date: 2025-02-06
Authors@R: person("Zuguang", "Gu", email = "z.gu@dkfz.de", role = c("aut", "cre"),
                  comment = c('ORCID'="0000-0002-7395-8709"))
Depends: R (>= 4.0.0)
Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
        2.5.4), matrixStats (>= 1.2.0), GetoptLong, circlize (>=
        0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer,
        cluster, skmeans, png, mclust, crayon, methods, xml2,
        microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6),
        digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr,
        foreach, doParallel, doRNG, irlba
Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen,
        NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE,
        AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree,
        dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot,
        flexclust, randomForest, e1071
Description: Subgroup classification is a basic task in genomic data
        analysis, especially for gene expression and DNA methylation
        data analysis. It can also be used to test the agreement to
        known clinical annotations, or to test whether there exist
        significant batch effects. The cola package provides a general
        framework for subgroup classification by consensus
        partitioning. It has the following features: 1. It modularizes
        the consensus partitioning processes that various methods can
        be easily integrated. 2. It provides rich visualizations for
        interpreting the results. 3. It allows running multiple methods
        at the same time and provides functionalities to
        straightforward compare results. 4. It provides a new method to
        extract features which are more efficient to separate
        subgroups. 5. It automatically generates detailed reports for
        the complete analysis. 6. It allows applying consensus
        partitioning in a hierarchical manner.
URL: https://github.com/jokergoo/cola,
        https://jokergoo.github.io/cola_collection/
VignetteBuilder: knitr
biocViews: Clustering, GeneExpression, Classification, Software
License: MIT + file LICENSE
LinkingTo: Rcpp
Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev perl
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:49:39 UTC
RemoteUrl: https://github.com/bioc/cola
RemoteRef: RELEASE_3_22
RemoteSha: 796a58f91c6a58dab1ffd405c38cf5fc54403a95
NeedsCompilation: yes
Packaged: 2025-11-11 13:49:02 UTC; root
Author: Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>)
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 13:56:45 UTC; windows
Archs: x64
