multiClust

DOI: 10.18129/B9.bioc.multiClust  

multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles

Bioconductor version: Release (3.16)

Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.

Author: Nathan Lawlor [aut, cre], Peiyong Guan [aut], Alec Fabbri [aut], Krish Karuturi [aut], Joshy George [aut]

Maintainer: Nathan Lawlor <nathan.lawlor03 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("multiClust")

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("multiClust")

 

HTML	R Script	A Guide to multiClust
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, FeatureExtraction, GeneExpression, Software, Survival
Version	1.28.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 years)
License	GPL (>= 2)
Depends
Imports	mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices
LinkingTo
Suggests	knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	multiClust_1.28.0.tar.gz
Windows Binary	multiClust_1.28.0.zip
macOS Binary (x86_64)	multiClust_1.28.0.tgz
macOS Binary (arm64)	multiClust_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/multiClust
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/multiClust
Bioc Package Browser	https://code.bioconductor.org/browse/multiClust/
Package Short Url	https://bioconductor.org/packages/multiClust/
Package Downloads Report	Download Stats