Package: CytoGLMM 1.21.0

Christof Seiler

CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments

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.

Authors:Christof Seiler [aut, cre]

CytoGLMM_1.21.0.tar.gz
CytoGLMM_1.21.0.zip(r-4.7)CytoGLMM_1.21.0.zip(r-4.6)CytoGLMM_1.21.0.zip(r-4.5)
CytoGLMM_1.21.0.tgz(r-4.6-any)CytoGLMM_1.21.0.tgz(r-4.5-any)
CytoGLMM_1.21.0.tar.gz(r-4.7-any)CytoGLMM_1.21.0.tar.gz(r-4.6-any)
CytoGLMM_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CytoGLMM/json (API)

# Install 'CytoGLMM' in R:

install.packages('CytoGLMM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/christofseiler/cytoglmm/issues

Pkgdown/docs site:https://christofseiler.github.io

On BioConductor:CytoGLMM-1.21.0(bioc 3.24)CytoGLMM-1.20.0(bioc 3.23)

flowcytometry proteomics singlecell cellbasedassays cellbiology immunooncology regression statisticalmethod software

6.03 score 3 stars 1 packages 2 scripts 4 mentions 11 exports 182 dependencies

Last updated from:b457ea4ed5. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	180
linux-devel-x86_64	NOTE	329
source / vignettes	OK	332
linux-release-x86_64	NOTE	281
macos-release-arm64	NOTE	125
macos-oldrel-arm64	NOTE	131
windows-devel	NOTE	207
windows-release	NOTE	173
windows-oldrel	NOTE	190
wasm-release	OK	206

Exports:cytoflexmix cytoglm cytoglmm cytogroup cytostab generate_data plot_heatmap plot_lda plot_mds plot_model_selection plot_prcomp

Dependencies:abind backports base64enc BH bigmemory bigmemory.sri BiocParallel boot broom bslib cachem car carData caret class cli clock cluster codetools colorspace commonmark corrplot cowplot cpp11 crosstalk curl data.table dendextend Deriv diagram digest doBy doParallel dplyr DT e1071 ellipse emmeans estimability evaluate factoextra FactoMineR farver fastmap flashClust flexmix fontawesome foreach forecast formatR Formula fracdiff fs futile.logger futile.options future future.apply generics ggplot2 ggpubr ggrepel ggsci ggsignif ggtext globals glue gower gridExtra gridtext gtable hardhat highr htmltools htmlwidgets ipred irlba isoband iterators jpeg jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lava lazyeval leaps lifecycle listenv litedown lme4 lmtest logging lubridate magrittr markdown MASS Matrix MatrixModels mbest memoise mgcv mime minqa ModelMetrics modelr modeltools multcompView mvtnorm nlme nloptr nnet numDeriv otel parallelly pbkrtest pheatmap pillar pkgconfig plyr png polynom pROC prodlim progressr promises proxy purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack recipes reformulas reshape2 rlang rmarkdown rpart rstatix S7 sandwich sass scales scatterplot3d shape showtext showtextdb snow SparseM sparsevctrs SQUAREM stringi stringr strucchange survival sysfonts tibble tidyr tidyselect timechange timeDate tinytex tzdb urca utf8 uuid vctrs viridis viridisLite withr xfun xml2 yaml zoo

CytoGLMM Workflow

Rendered fromCytoGLMM.Rmdusingknitr::rmarkdown

Last update: 2025-07-18
Started: 2019-02-27

Help page	Topics
Check if input to cytoxxx function have errors	cyto_check
Logistic mixture regression	cytoflexmix
Fit GLM with bootstrap resampling	cytoglm
Fit GLMM with method of moments	cytoglmm
Group-specific fixed effects model	cytogroup
Evaluate parameter stability with respect to gating sheme	cytostab
Generate dataset for vignettes and simulation studies	generate_data
Generalized linear mixed model with maximum likelihood	glmm_moment
Check if samples match or paired on condition	is_unpaired
Helper function to plot regression coeffcient	plot_coeff
Heatmap of median marker expression	plot_heatmap
LDA on marker expression	plot_lda
MDS on median marker expression	plot_mds
Plot model selection to choose number optimal number of clusters	plot_model_selection
Plot PCA of subsampled data using ggplot	plot_prcomp
Plot all components of mixture regression	plot.cytoflexmix
Plot bootstraped coefficients	plot.cytoglm
Plot fixded coefficients of random effects model	plot.cytoglmm
Plot fixded coefficients of group-specific fixed effects model	plot.cytogroup
Extact and print bootstrap GLM fit	print.cytoglm
Extact and print GLMM fit	print.cytoglmm
Remove samples based on low cell counts	remove_samples
Extact and calculate p-values of bootstrap GLM fit	summary.cytoglm
Extact and calculate p-values of GLMM fit	summary.cytoglmm

Package: CytoGLMM 1.21.0

CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments

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