Package: sccomp 2.5.0

Stefano Mangiola

sccomp: Differential Composition and Variability Analysis for Single-Cell Data

Comprehensive R package for differential composition and variability analysis in single-cell RNA sequencing, CyTOF, and microbiome data. Provides robust Bayesian modeling with outlier detection, random effects, and advanced statistical methods for cell type proportion analysis. Features include probabilistic outlier identification, mixed-effect modeling, differential variability testing, and comprehensive visualization tools. Perfect for cancer research, immunology, developmental biology, and single-cell genomics applications.

Authors:Stefano Mangiola [aut, cre], Alexandra J. Roth-Schulze [aut], Marie Trussart [aut], Enrique Zozaya-Valdés [aut], Mengyao Ma [aut], Zijie Gao [aut], Alan F. Rubin [aut], Terence P. Speed [aut], Heejung Shim [aut], Anthony T. Papenfuss [aut]

sccomp_2.5.0.tar.gz
sccomp_2.5.0.zip(r-4.7)sccomp_2.5.0.zip(r-4.6)sccomp_2.5.0.zip(r-4.5)
sccomp_2.5.0.tgz(r-4.6-any)sccomp_2.5.0.tgz(r-4.5-any)
sccomp_2.5.0.tar.gz(r-4.7-any)sccomp_2.5.0.tar.gz(r-4.6-any)
sccomp_2.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
sccomp/json (API)

# Install 'sccomp' in R:
install.packages('sccomp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mangiolalaboratory/sccomp/issues

Datasets:

On BioConductor:sccomp-2.5.0(bioc 3.24)sccomp-2.4.0(bioc 3.23)

bayesianregressiondifferentialexpressionsinglecellmetagenomicsflowcytometryspatialbatch-correctioncompositioncytofdifferential-proportionmicrobiomemultilevelproportionsrandom-effectssingle-cellunwanted-variation

8.88 score 125 stars 168 scripts 460 downloads 16 exports 67 dependencies

Last updated from:67110133c8. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR218
linux-devel-x86_64NOTE364
source / vignettesOK277
linux-release-x86_64NOTE407
macos-release-arm64NOTE317
macos-oldrel-arm64NOTE252
windows-develNOTE360
windows-releaseNOTE278
windows-oldrelNOTE263
wasm-releaseOK186

Exports:clear_stan_model_cacheplot_1D_intervalsplot_2D_intervalssccomp_boxplotsccomp_calculate_residualssccomp_estimatesccomp_predictsccomp_proportional_fold_changesccomp_remove_outlierssccomp_remove_unwanted_effectssccomp_remove_unwanted_variationsccomp_replicatesccomp_stan_models_cache_dirsccomp_testsccomp_themesimulate_data

Dependencies:abindBiobaseBiocGenericsbitbit64bootcallrclicliprcpp11crayonDelayedArraydplyrfansifarverforcatsfsgenericsGenomicRangesggplot2ggrepelgluegtablehmsinstantiateIRangesisobandlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspatchworkpillarpkgconfigprettyunitsprocessxprogresspspurrrR6RColorBrewerRcppreadrrlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXVector

sccomp: Differential Composition and Variability Analysis for Single-Cell Data

Stefano Mangiola

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 16 2026.

Last update: 2025-07-18
Started: 2021-09-19