kmcut
This is the development version of kmcut; for the stable release version, see kmcut.
Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers
Bioconductor version: Development (3.24)
The purpose of the package is to identify prognostic biomarkers and an optimal numeric cutoff for each biomarker that can be used to stratify a group of test subjects (samples) into two sub-groups with significantly different survival (better vs. worse). The package was developed for the analysis of gene expression data, such as RNA-seq. However, it can be used with any quantitative variable that has a sufficiently large proportion of unique values.
Author: Igor Kuznetsov [aut, cre], Javed Khan [aut]
Maintainer: Igor Kuznetsov <ibkalb at gmail.com>
citation("kmcut")):
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("kmcut")
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("kmcut")| kmcut_intro | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Software, StatisticalMethod, Survival |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | survival, tools, methods, pracma, doParallel, foreach, parallel, SummarizedExperiment, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| 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 | kmcut_1.7.0.tar.gz |
| Windows Binary (x86_64) | kmcut_1.7.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | kmcut_1.7.0.tgz |
| macOS Binary (sonoma-arm64) | kmcut_1.7.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/kmcut |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/kmcut |
| Bioc Package Browser | https://code.bioconductor.org/browse/kmcut/ |
| Package Short Url | https://bioconductor.org/packages/kmcut/ |
| Package Downloads Report | Download Stats |