cola
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see cola.
A Framework for Consensus and Hierarchical Partitioning
Bioconductor version: 3.9
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("cola")):
Installation
To install this package, start R (version "3.6") 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 Using cola Package | HTML | R Script |
| 2. A Framework for Consensus and Hierarchical Partitioning | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, GeneExpression, Software |
| Version | 1.0.1 |
| 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(>= 2.0.0), 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 |
| System Requirements | |
| URL | https://github.com/jokergoo/cola |
See More
| Suggests | genefilter, mvtnorm, testthat (>= 0.3), data.tree, dendextend, samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, AnnotationDbi, gplots |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cola_1.0.1.tar.gz |
| Windows Binary | cola_1.0.1.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | cola_1.0.1.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 3.9 | Source Archive |