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CytoGLMM

Conditional Differential Analysis for Flow and Mass Cytometry Experiments


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
CytoGLMM Workflow HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, CellBiology, FlowCytometry, ImmunoOncology, Proteomics, Regression, SingleCell, Software, StatisticalMethod
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License LGPL-3
Depends
Imports stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices
System Requirements
URL https://christofseiler.github.io/CytoGLMM https://github.com/ChristofSeiler/CytoGLMM
Bug Reports https://github.com/ChristofSeiler/CytoGLMM/issues
See More
Suggests knitr, rmarkdown, testthat, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me CyTOFpower
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CytoGLMM_1.10.0.tar.gz
Windows Binary CytoGLMM_1.10.0.zip
macOS Binary (x86_64) CytoGLMM_1.10.0.tgz
macOS Binary (arm64) CytoGLMM_1.10.0.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