Package: censcyt 1.15.0

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_1.15.0.tar.gz
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censcyt.pdf |censcyt.html✨
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-1.15.0(bioc 3.21)censcyt-1.14.0(bioc 3.20)

immunooncology flowcytometry proteomics singlecell cellbasedassays cellbiology clustering featureextraction software survival

4.30 score 2 scripts 151 downloads 6 exports 169 dependencies

Last updated 2 months agofrom:22cee1daf1. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:censcyt conditional_multiple_imputation createFormula simulate_multicluster simulate_singlecluster testDA_censoredGLMM

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

Censored covariate in cytometry

Reto Gerber

Rendered fromcensored_covariate.Rmdusingknitr::rmarkdownon Nov 29 2024.

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