Package: CytoGLMM 1.13.0

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]

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CytoGLMM/json (API)
NEWS

# 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

On BioConductor:CytoGLMM-1.13.0(bioc 3.20)CytoGLMM-1.12.0(bioc 3.19)

bioconductor-package

11 exports 0.82 score 158 dependencies 1 dependents 4 mentions

Last updated 2 months agofrom:8559ef8c8d

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 corrplot cowplot cpp11 crosstalk data.table dendextend diagram digest doParallel dplyr DT e1071 ellipse ellipsis emmeans estimability evaluate factoextra FactoMineR fansi farver fastmap flashClust flexmix fontawesome foreach formatR fs futile.logger futile.options future future.apply generics ggplot2 ggpubr ggrepel ggsci ggsignif globals glue gower gridExtra gtable hardhat highr htmltools htmlwidgets httpuv ipred isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lava lazyeval leaps lifecycle listenv lme4 logging lubridate magrittr MASS Matrix MatrixModels mbest memoise mgcv mime minqa ModelMetrics modeltools multcompView munsell mvtnorm nlme nloptr nnet numDeriv parallelly pbkrtest pheatmap pillar pkgconfig plyr polynom pROC prodlim progressr promises proxy purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen recipes reshape2 rlang rmarkdown rpart rstatix sandwich sass scales scatterplot3d shape snow SparseM SQUAREM stringi stringr strucchange survival tibble tidyr tidyselect timechange timeDate tinytex tzdb utf8 uuid vctrs viridis viridisLite withr xfun yaml zoo

CytoGLMM Workflow

Christof Seiler

Rendered fromCytoGLMM.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-04-05
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 1.13.0

CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments

CytoGLMM Workflow

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