Package: cola
Type: Package
Title: A Framework for Consensus and Hierarchical Partitioning
Version: 1.0.1
Date: 2019-09-16
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Depends: R (>= 3.6.0)
Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
        2.0.0), matrixStats, GetoptLong, circlize (>= 0.4.7),
        GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer,
        cluster, skmeans, png, mclust, crayon, methods, xml2,
        microbenchmark, httr, knitr, markdown, digest, impute, brew,
        Rcpp (>= 0.11.0), BiocGenerics, eulerr
Suggests: genefilter, mvtnorm, testthat (>= 0.3), data.tree,
        dendextend, samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap,
        clusterProfiler, AnnotationDbi, gplots
Description: Subgroup classification is a basic task in genomic data analysis,
  especially for gene expression data and methylation data. It can predict
  novel subgroups when there is nothing known about the data or it can test
  consistency between predicted subgroups with known annotations. The cola
  package provides a general framework for subgroup classification by
  consensus clustering. It has following features: 1. It modularizes the
  consensus clustering 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 compare results in a straightforward way. 4. It provides
  a new method to extract features which are more efficient to separate
  subgroups. 5. It allows doing partitioning in a hierarchical way to detect
  subgroups with relatively smaller difference. 6. It generates detailed
  reports for the complete analysis.
URL: https://github.com/jokergoo/cola
VignetteBuilder: knitr
biocViews: Clustering, GeneExpression, Classification, Software
License: MIT + file LICENSE
LinkingTo: Rcpp
git_url: https://git.bioconductor.org/packages/cola
git_branch: RELEASE_3_9
git_last_commit: db87ed6
git_last_commit_date: 2019-09-16
Date/Publication: 2019-09-16
NeedsCompilation: yes
Packaged: 2019-09-17 05:22:50 UTC; biocbuild
Built: R 3.6.1; i386-w64-mingw32; 2019-09-17 12:48:19 UTC; windows
Archs: i386, x64
