Conditional Differential Analysis for Flow and Mass Cytometry Experiments

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Documentation for package ‘CytoGLMM’ version 1.13.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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