censcyt

DOI: 10.18129/B9.bioc.censcyt  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	Censored covariate
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software, Survival
Version	1.6.1
In Bioconductor since	BioC 3.13 (R-4.1) (2 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, ggplot2
SystemRequirements
Enhances
URL	https://github.com/retogerber/censcyt
BugReports	https://github.com/retogerber/censcyt/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	censcyt_1.6.1.tar.gz
Windows Binary	censcyt_1.6.1.zip
macOS Binary (x86_64)	censcyt_1.6.1.tgz
macOS Binary (arm64)	censcyt_1.6.1.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
Old Source Packages for BioC 3.16	Source Archive