censcyt

DOI: 10.18129/B9.bioc.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 (3.14)

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 "4.1") and enter:

if (!requireNamespace("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")

 

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 1.1.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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_1.1.0.tar.gz
Windows Binary censcyt_1.1.0.zip
macOS 10.13 (High Sierra) censcyt_1.1.0.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

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