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.
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.
To install from bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("censcyt")
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")