cola

DOI: 10.18129/B9.bioc.cola    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see cola.

A Framework for Consensus Partitioning

Bioconductor version: 3.14

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.

Author: Zuguang Gu

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

Installation

To install this package, start R (version "4.1") and enter:

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

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		Use of cola
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, Clustering, GeneExpression, Software
Version	2.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (3 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0)
Imports	grDevices, graphics, grid, stats, utils, ComplexHeatmap(>= 2.5.4), 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, foreach, doParallel, irlba
LinkingTo	Rcpp
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
SystemRequirements
Enhances
URL	https://github.com/jokergoo/cola https://jokergoo.github.io/cola_collection/
Depends On Me
Imports Me
Suggests Me	InteractiveComplexHeatmap, simplifyEnrichment
Links To Me
Build Report

Package Archives

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

Source Package	cola_2.0.0.tar.gz
Windows Binary	cola_2.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	cola_2.0.0.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	https://bioconductor.org/packages/cola/
Package Downloads Report	Download Stats