CytoGLMM

DOI: 10.18129/B9.bioc.CytoGLMM    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CytoGLMM.

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Bioconductor version: 3.13

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 "4.1") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CytoGLMM_1.0.0.tar.gz
Windows Binary CytoGLMM_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) CytoGLMM_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CytoGLMM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CytoGLMM
Package Short Url https://bioconductor.org/packages/CytoGLMM/
Package Downloads Report Download Stats

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