CytoGLMM

DOI: 10.18129/B9.bioc.CytoGLMM  

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Bioconductor version: Release (3.16)

The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.

Author: Christof Seiler [aut, cre]

Maintainer: Christof Seiler <christof.seiler at maastrichtuniversity.nl>

Installation

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

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

BiocManager::install("CytoGLMM")

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("CytoGLMM")

 

HTML	R Script	CytoGLMM Workflow
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, CellBiology, FlowCytometry, ImmunoOncology, Proteomics, Regression, SingleCell, Software, StatisticalMethod
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	LGPL-3
Depends
Imports	stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, speedglm, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL	https://christofseiler.github.io/CytoGLMM https://github.com/ChristofSeiler/CytoGLMM
BugReports	https://github.com/ChristofSeiler/CytoGLMM/issues
Depends On Me
Imports Me	CyTOFpower
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CytoGLMM_1.6.0.tar.gz
Windows Binary	CytoGLMM_1.6.0.zip
macOS Binary (x86_64)	CytoGLMM_1.6.0.tgz
macOS Binary (arm64)	CytoGLMM_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CytoGLMM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CytoGLMM
Bioc Package Browser	https://code.bioconductor.org/browse/CytoGLMM/
Package Short Url	https://bioconductor.org/packages/CytoGLMM/
Package Downloads Report	Download Stats