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("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 | ||
| 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 | |
| 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_1.6.0.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 |