Package: CytoGLMM 1.15.0

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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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

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

On BioConductor:CytoGLMM-1.15.0(bioc 3.21)CytoGLMM-1.14.0(bioc 3.20)

flowcytometryproteomicssinglecellcellbasedassayscellbiologyimmunooncologyregressionstatisticalmethodsoftware

5.68 score 2 stars 1 packages 1 scripts 234 downloads 4 mentions 11 exports 166 dependencies

Last updated 4 months agofrom:a3b4bb6e45. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 27 2025
R-4.5-winNOTEFeb 27 2025
R-4.5-macNOTEFeb 27 2025
R-4.5-linuxNOTEFeb 27 2025
R-4.4-winNOTEFeb 27 2025
R-4.4-macNOTEFeb 27 2025
R-4.3-winNOTEFeb 27 2025
R-4.3-macNOTEFeb 27 2025

Exports:cytoflexmixcytoglmcytoglmmcytogroupcytostabgenerate_dataplot_heatmapplot_ldaplot_mdsplot_model_selectionplot_prcomp

Dependencies:abindbackportsbase64encBHbigmemorybigmemory.sriBiocParallelbootbroombslibcachemcarcarDatacaretclasscliclockclustercodetoolscolorspacecorrplotcowplotcpp11crosstalkdata.tabledendextendDerivdiagramdigestdoBydoParalleldplyrDTe1071ellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustflexmixfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygenericsggplot2ggpubrggrepelggsciggsignifglobalsgluegowergridExtragtablehardhathighrhtmltoolshtmlwidgetshttpuvipredisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelavalazyevalleapslifecyclelistenvlme4logginglubridatemagrittrMASSMatrixMatrixModelsmbestmemoisemgcvmicrobenchmarkmimeminqaModelMetricsmodelrmodeltoolsmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivparallellypbkrtestpheatmappillarpkgconfigplyrpolynompROCprodlimprogressrpromisesproxypurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackrecipesreformulasreshape2rlangrmarkdownrpartrstatixsandwichsassscalesscatterplot3dshapesnowSparseMsparsevctrsSQUAREMstringistringrstrucchangesurvivaltibbletidyrtidyselecttimechangetimeDatetinytextzdbutf8uuidvctrsviridisviridisLitewithrxfunyamlzoo

CytoGLMM Workflow

Rendered fromCytoGLMM.Rmdusingknitr::rmarkdownon Feb 27 2025.

Last update: 2021-04-05
Started: 2019-02-27