README.md

In retogerber/censcyt: Differential abundance analysis with a right censored covariate in high-dimensional cytometry

censcyt

Summary

censcyt is an R package extending the diffcyt (differential discovery in high-dimensional cytometry via high-resolution clustering) pipeline. censcyt (Censored diffcyt) includes methods for differential abundance analysis in the presence of a covariate subject to right censoring. It uses the reversed association testing approach (like diffcyt) meaning the censored variable (e.g. survival time) is modeled as a predictor. Classical survival analysis methods on the other hand model the censored variable as the response. See also here.

Vignettes

The main workflow can be found in the Bioconductor package vignette of diffcyt. An example use of the censcyt methods for differential abundance analysis with a covariate subject to right censoring is available in the package vignette on bioconductor.

Install

To install from bioconductor:

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

BiocManager::install("censcyt")

Development version

To install directly from GitHub run the following code:

# First install 'devtools' package from CRAN
install.packages("devtools")

# Then install 'censcyt' package from GitHub
devtools::install_github("retogerber/censcyt")

retogerber/censcyt documentation built on Feb. 7, 2023, 9:56 a.m.