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✨
DESCRIPTION |NEWS
card.svg |card.png
censcyt/json (API)

# 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 2 scripts 6 exports 171 dependencies

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

Target	Result	Time
bioc-checks	NOTE	232
linux-devel-x86_64	NOTE	455
source / vignettes	OK	315
linux-release-x86_64	NOTE	461
macos-release-arm64	NOTE	367
macos-oldrel-arm64	NOTE	246
windows-devel	NOTE	322
windows-release	NOTE	326
windows-oldrel	NOTE	312
wasm-release	OK	235

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 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

Rendered fromcensored_covariate.Rmdusingknitr::rmarkdown

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