survClust
This is the development version of survClust; for the stable release version, see survClust.
Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning
Bioconductor version: Development (3.24)
survClust is an outcome weighted integrative clustering algorithm used to classify multi-omic samples on their available time to event information. The resulting clusters are cross-validated to avoid over overfitting and output classification of samples that are molecularly distinct and clinically meaningful. It takes in binary (mutation) as well as continuous data (other omic types).
Author: Arshi Arora [aut, cre]
Maintainer: Arshi Arora <arshiaurora at gmail.com>
citation("survClust")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("survClust")
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("survClust")| An introduction to survClust package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, Software, Survival |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | Rcpp, MultiAssayExperiment, pdist, survival |
| System Requirements | |
| URL | https://github.com/arorarshi/survClust |
| Bug Reports | https://support.bioconductor.org/t/survClust |
See More
| Suggests | knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel |
| 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 | survClust_1.7.0.tar.gz |
| Windows Binary (x86_64) | survClust_1.7.0.zip |
| macOS Binary (big-sur-x86_64) | survClust_1.7.0.tgz |
| macOS Binary (sonoma-arm64) | survClust_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/survClust |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/survClust |
| Bioc Package Browser | https://code.bioconductor.org/browse/survClust/ |
| Package Short Url | https://bioconductor.org/packages/survClust/ |
| Package Downloads Report | Download Stats |