censcyt

This is the released version of censcyt; for the devel version, see censcyt.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

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

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-5414-8906

Maintainer: Reto Gerber <gerberreto at pm.me>

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

Reto Gerber. censcyt: Differential abundance analysis with a right censored covariate in high-dimensional cytometry. doi:10.18129/B9.bioc.censcyt, R package version 1.20.0, https://bioconductor.org/packages/censcyt.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FeatureExtraction, FlowCytometry, ImmunoOncology, Proteomics, SingleCell, Software, Survival
Version	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 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

Suggests	BiocStyle, knitr, rmarkdown, testthat, ggplot2
Linking To
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	censcyt_1.20.0.tar.gz
Windows Binary (x86_64)	censcyt_1.20.0.zip
macOS Binary (big-sur-x86_64)	censcyt_1.20.0.tgz
macOS Binary (sonoma-arm64)	censcyt_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/censcyt
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/censcyt
Package Short Url	https://bioconductor.org/packages/censcyt/
Package Downloads Report	Download Stats