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:
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)
immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftwaresurvival
Last updated 3 months agofrom:22cee1daf1. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | WARNING | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | NOTE | Jan 28 2025 |
| R-4.4-mac | NOTE | Jan 28 2025 |
| R-4.3-win | NOTE | Jan 28 2025 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:censcytconditional_multiple_imputationcreateFormulasimulate_multiclustersimulate_singleclustertestDA_censoredGLMM
Dependencies:abindALLaskpassbackportsBHBiobaseBiocGenericsBiocParallelbitbit64bootbroombroom.mixedcarcarDatacirclizeclicliprclueclustercodacodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncurlcytolibDelayedArrayDerivdiffcytdigestdirmultdoBydoParalleldplyredgeRfansifarverfitdistrplusflowCoreFlowSOMforcatsforeachformatRFormulafurrrfutile.loggerfutile.optionsfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggforceggnewscaleggplot2ggpubrggrepelggsciggsignifglmnetGlobalOptionsglobalsgluegridExtragtablehavenhmshttrigraphIRangesisobanditeratorsjomojsonlitelabelinglambda.rlatticelifecyclelimmalistenvlme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicemicrobenchmarkmimeminqamitmlmodelrmultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslordinalpanparallellypbkrtestpillarpkgconfigplyrpngpolyclippolynomprettyunitsprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreadrreformulasreshape2Rhdf5librjsonrlangrpartRProtoBufLibrstatixRtsneS4ArraysS4VectorssandwichscalesshapesnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontsTH.datatibbletidyrtidyselecttweenrtzdbucminfUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectorzoo
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 |