multiClust
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Bioconductor version: Release (3.19)
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>
citation("multiClust")):
Installation
To install this package, start R (version "4.4") 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")| A Guide to multiClust | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, FeatureExtraction, GeneExpression, Software, Survival |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 years) |
| License | GPL (>= 2) |
| Depends | |
| Imports | mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery |
| Linking To | |
| 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 | multiClust_1.34.0.tar.gz |
| Windows Binary (x86_64) | multiClust_1.34.0.zip |
| macOS Binary (x86_64) | multiClust_1.34.0.tgz |
| macOS Binary (arm64) | multiClust_1.34.0.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 |