cola

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see cola.

A Framework for Consensus Partitioning


Bioconductor version: 3.12

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.

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 "4.0") 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")
1. A Quick Start of cola Package HTML R Script
2. cola: A Framework for Consensus Partitioning HTML R Script
3. Automatic Functional Enrichment on Signature Genes HTML R Script
4. Predict Classes for New Samples HTML R Script
5. Work with Big Datasets HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, Clustering, GeneExpression, Software
Version 1.6.0
In Bioconductor since BioC 3.9 (R-3.6) (5 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
System Requirements
URL https://github.com/jokergoo/cola https://jokergoo.github.io/cola_collection/
See More
Suggests genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend
Linking To Rcpp
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package cola_1.6.0.tar.gz
Windows Binary cola_1.6.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) cola_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cola
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cola
Bioc Package Browser https://code.bioconductor.org/browse/cola/
Package Short Url https://bioconductor.org/packages/cola/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive