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Bioconductor - cola (development version)

cola

This is the development version of cola; for the stable release version, see cola.

A Framework for Consensus Partitioning

Bioconductor version: Development (3.22)

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 [aut, cre] ORCID: 0000-0002-7395-8709

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

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

To install this package, start R (version "4.5") and enter:


if (!require("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")

Details biocViews Classification, Clustering, GeneExpression, Software Version 2.15.0 In Bioconductor since BioC 3.9 (R-3.6) (6 years) License MIT + file LICENSE 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 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, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 Linking To Rcpp Enhances Depends On Me Imports Me Suggests Me InteractiveComplexHeatmap, simplifyEnrichment Links To Me Build Report Build Report Package Archives

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

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