cola

DOI: 10.18129/B9.bioc.cola    

This is the development version of cola; to use it, please install the devel version of Bioconductor.

A Framework for Consensus and Hierarchical Partitioning

Bioconductor version: Development (3.10)

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.

Author: Zuguang Gu

Maintainer: Zuguang Gu <z.gu at dkfz.de>

Citation (from within R, enter citation("cola")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("cola")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cola")

 

HTML R Script 1. A Quick Start of Using cola Package
HTML R Script 2. A Framework for Consensus and Hierarchical Partitioning
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Classification, Clustering, GeneExpression, Software
Version 1.1.2
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License MIT + file LICENSE
Depends R (>= 3.3.0)
Imports grDevices, graphics, grid, stats, utils, ComplexHeatmap(>= 1.99.0), matrixStats, GetoptLong, circlize (>= 0.4.5), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, gplots, mclust, crayon, methods, xml2, microbenchmark, httr, knitr, markdown, digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr
LinkingTo Rcpp
Suggests genefilter, mvtnorm, testthat (>= 0.3), data.tree, dendextend, samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, AnnotationDbi
SystemRequirements
Enhances
URL https://github.com/jokergoo/cola
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cola_1.1.2.tar.gz
Windows Binary cola_1.1.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) cola_1.1.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/cola
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cola
Package Short Url http://bioconductor.org/packages/cola/
Package Downloads Report Download Stats

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