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censcyt

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

Bioconductor version: Release (3.17)

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 "4.3") 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")
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 1.8.0
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
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat, ggplot2
System Requirements
Enhances
URL https://github.com/retogerber/censcyt
Bug Reports https://github.com/retogerber/censcyt/issues
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Build Report  

Package Archives

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

Source Package censcyt_1.8.0.tar.gz
Windows Binary censcyt_1.8.0.zip
macOS Binary (x86_64) censcyt_1.8.0.tgz
macOS Binary (arm64) censcyt_1.8.0.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