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censcyt

This is the development version of censcyt; for the stable release version, see censcyt.

Differential abundance analysis with a right censored covariate in high-dimensional cytometry


Bioconductor version: Development (3.19)

Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.

Author: Reto Gerber [aut, cre]

Maintainer: Reto Gerber <gerberreto at pm.me>

Citation (from within R, enter citation("censcyt")):

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("censcyt")

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("censcyt")
Censored covariate HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software, Survival
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.0), diffcyt
Imports BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils
System Requirements
URL https://github.com/retogerber/censcyt
Bug Reports https://github.com/retogerber/censcyt/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat, ggplot2
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package censcyt_1.11.0.tar.gz
Windows Binary censcyt_1.11.0.zip
macOS Binary (x86_64) censcyt_1.11.0.tgz
macOS Binary (arm64) censcyt_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/censcyt
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/censcyt
Bioc Package Browser https://code.bioconductor.org/browse/censcyt/
Package Short Url https://bioconductor.org/packages/censcyt/
Package Downloads Report Download Stats