Package: sccomp 1.99.10

Stefano Mangiola

sccomp: Tests differences in cell-type proportion for single-cell data, robust to outliers

A robust and outlier-aware method for testing differences in cell-type proportion in single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.

Authors:Stefano Mangiola [aut, cre]

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sccomp.pdf |sccomp.html✨
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-1.99.8(bioc 3.21)sccomp-1.10.0(bioc 3.20)

bayesianregressiondifferentialexpressionsinglecellbatch-correctioncompositioncytofdifferential-proportionmicrobiomemultilevelproportionsrandom-effectssingle-cellunwanted-variation

8.32 score 97 stars 69 scripts 246 downloads 13 exports 80 dependencies

Last updated 23 days agofrom:cfa80501ea. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winNOTEJan 29 2025
R-4.5-macWARNINGJan 29 2025
R-4.5-linuxNOTEJan 29 2025
R-4.4-winNOTEJan 29 2025
R-4.4-macNOTEJan 29 2025
R-4.3-winNOTEJan 29 2025
R-4.3-macNOTEJan 29 2025

Exports:get_output_samplesplot_1D_intervalsplot_2D_intervalssccomp_boxplotsccomp_calculate_residualssccomp_estimatesccomp_predictsccomp_proportional_fold_changesccomp_remove_outlierssccomp_remove_unwanted_variationsccomp_replicatesccomp_testsimulate_data

Dependencies:abindaskpassBiobaseBiocGenericsbitbit64bootcallrclicliprcolorspacecpp11crayoncurlDelayedArraydplyrfansifarverforcatsfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtablehmshttrinstantiateIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigprettyunitsprocessxprogresspspurrrR6RColorBrewerRcppreadrrlangS4ArraysS4VectorsscalesSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVector

Overview of the sccomp package

Stefano Mangiola

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2025-01-23
Started: 2021-09-19