kmcut

Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers

Bioconductor version: Release (3.20)

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 (from within R, enter citation("kmcut")):

Installation

To install this package, start R (version "4.4") and enter:


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

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Software, StatisticalMethod, Survival
Version	1.0.0
In Bioconductor since	BioC 3.20 (R-4.4) (< 6 months)
License	Artistic-2.0
Depends
Imports	survival, tools, methods, pracma, doParallel, foreach, parallel, SummarizedExperiment, S4Vectors
System Requirements
URL

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_1.0.0.tar.gz
Windows Binary (x86_64)	kmcut_1.0.0.zip
macOS Binary (x86_64)	kmcut_1.0.0.tgz
macOS Binary (arm64)	kmcut_0.99.5.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