CytoGLMM
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see CytoGLMM.
Conditional Differential Analysis for Flow and Mass Cytometry Experiments
Bioconductor version: 3.14
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("CytoGLMM")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, CellBiology, FlowCytometry, ImmunoOncology, Proteomics, Regression, SingleCell, Software, StatisticalMethod |
| Version | 1.2.0 |
| 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, speedglm, 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_1.2.0.tar.gz |
| Windows Binary | CytoGLMM_1.2.0.zip |
| macOS 10.13 (High Sierra) | CytoGLMM_1.2.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |