Package: censcyt 1.21.0

Reto Gerber

censcyt: Differential abundance analysis with a right censored covariate in high-dimensional cytometry

Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.

Authors:Reto Gerber [aut, cre]

censcyt_1.21.0.tar.gz
censcyt_1.21.0.zip(r-4.7)censcyt_1.21.0.zip(r-4.6)censcyt_1.21.0.zip(r-4.5)
censcyt_1.21.0.tgz(r-4.6-any)censcyt_1.21.0.tgz(r-4.5-any)
censcyt_1.21.0.tar.gz(r-4.7-any)censcyt_1.21.0.tar.gz(r-4.6-any)
censcyt_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
censcyt/json (API)
NEWS

# Install 'censcyt' in R:

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

Bug tracker:https://github.com/retogerber/censcyt/issues

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

immunooncology flowcytometry proteomics singlecell cellbasedassays cellbiology clustering featureextraction software survival

4.30 score 7 scripts 312 downloads 6 exports 172 dependencies

Last updated from:8bd67697e5. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	238
linux-devel-x86_64	NOTE	445
source / vignettes	OK	378
linux-release-x86_64	NOTE	454
macos-release-arm64	NOTE	263
macos-oldrel-arm64	NOTE	269
windows-devel	NOTE	348
windows-release	NOTE	324
windows-oldrel	NOTE	325
wasm-release	OK	192

Exports:censcyt conditional_multiple_imputation createFormula simulate_multicluster simulate_singlecluster testDA_censoredGLMM

Dependencies:abind ALL backports base64enc BH Biobase BiocGenerics biocmake BiocParallel bit bit64 boot broom broom.mixed car carData circlize cli clipr clue cluster coda codetools colorRamps colorspace ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon cytolib DelayedArray Deriv diffcyt digest dir.expiry dirmult doBy doParallel dplyr edgeR farver filelock fitdistrplus flowCore FlowSOM forcats foreach forecast formatR Formula fracdiff furrr futile.logger futile.options future generics GenomicRanges GetoptLong ggforce ggnewscale ggplot2 ggpubr ggrepel ggsci ggsignif glmnet GlobalOptions globals glue gridExtra gtable haven hms igraph IRanges isoband iterators jomo jsonlite labeling lambda.r lattice lifecycle limma listenv lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv mice microbenchmark minqa mitml modelr multcomp mvtnorm nlme nloptr nnet numDeriv ordinal pan parallelly pbkrtest pillar pkgconfig plyr png polyclip polynom prettyunits progress purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas reshape2 Rhdf5lib rjson rlang rpart RProtoBufLib rstatix Rtsne S4Arrays S4Vectors S7 sandwich scales Seqinfo shape snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival systemfonts TH.data tibble tidyr tidyselect timeDate tweenr tzdb ucminf urca utf8 vctrs viridisLite vroom withr XML XVector zoo

Censored covariate in cytometry

Reto Gerber

Rendered fromcensored_covariate.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2020-12-08
Started: 2020-10-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Run 'censcyt' pipeline	censcyt-package censcyt
Conditional multiple imputation	conditional_multiple_imputation
Create model formula and corresponding data frame of variables	createFormula
Simulate multicluster counts with time dependent association from a Dirichlet-Multinomial distribution	simulate_multicluster
Simulation of data with a censored covariate	simulate_singlecluster
Test for differential abundance: method 'censcyt-DA-censored-GLMM'	testDA_censoredGLMM