censcyt

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see censcyt.

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

Bioconductor version: 3.21

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 iD ORCID: 0000-0001-5414-8906

Maintainer: Reto Gerber <gerberreto at pm.me>

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

Installation

To install this package, start R (version "4.5") 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 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 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

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package censcyt_1.16.0.tar.gz

Windows Binary (x86_64) censcyt_1.16.0.zip

macOS Binary (x86_64) censcyt_1.16.0.tgz

macOS Binary (arm64) censcyt_1.16.0.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