Package: sccomp 1.11.0

Stefano Mangiola

sccomp: Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

A robust and outlier-aware method for testing differential tissue composition from 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'))

Peer review:

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

Datasets:

On BioConductor:sccomp-1.11.0(bioc 3.21)sccomp-1.10.0(bioc 3.20)

bayesianregressiondifferentialexpressionsinglecellbatch-correctioncompositioncytofdifferential-proportionmicrobiomemultilevelproportionsrandom-effectssingle-cellunwanted-variation

8.24 score 93 stars 59 scripts 195 downloads 13 exports 94 dependencies

Last updated 21 days agofrom:4f2a9618bd. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

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:abindaskpassBiobaseBiocGenericsbitbit64bootcallrclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydigestdotCall64dplyrfansifarverforcatsfsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelglobalsgluegtablehmshttrinstantiateIRangesisobandjsonlitelabelinglatticelifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslparallellypatchworkpillarpkgconfigprettyunitsprocessxprogressprogressrpspurrrR6RColorBrewerRcppRcppEigenreadrrlangS4ArraysS4VectorsscalesSeuratObjectSingleCellExperimentspspamSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectorzlibbioc

Overview of the sccomp package

Stefano Mangiola

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-10-12
Started: 2021-09-19