Package: spillR 1.3.0

Marco Guazzini

spillR: Spillover Compensation in Mass Cytometry Data

Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

Authors:Marco Guazzini [aut, cre], Alexander G. Reisach [aut], Sebastian Weichwald [aut], Christof Seiler [aut]

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spillR.pdf |spillR.html✨
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NEWS

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

On BioConductor:spillR-1.3.0(bioc 3.21)spillR-1.2.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

flowcytometryimmunooncologymassspectrometrypreprocessingsinglecellsoftwarestatisticalmethodvisualizationregression

4.48 score 3 scripts 158 downloads 4 exports 174 dependencies

Last updated 5 months agofrom:7a34e976ca. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 28 2025
R-4.5-winOKFeb 28 2025
R-4.5-macOKFeb 28 2025
R-4.5-linuxOKFeb 28 2025
R-4.4-winOKFeb 28 2025
R-4.4-macOKFeb 28 2025
R-4.3-winOKFeb 28 2025
R-4.3-macOKFeb 28 2025

Exports:compCytofgenerate_beadgenerate_realplotDiagnostics

Dependencies:abindALLaskpassassortheadbackportsbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbootbroomCairocarcarDataCATALYSTcirclizecliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncurlcytolibdata.tableDelayedArrayDerivdigestdoBydoParalleldplyrdqrngdrcfansifarverflowCoreFlowSOMFNNforeachformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggforceggnewscaleggplot2ggpubrggrastrggrepelggridgesggsciggsignifGlobalOptionsgluegridExtragtablegtoolshttrigraphIRangesirlbaisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnnlsnumDerivopensslpbkrtestpheatmappillarpkgconfigplotrixplyrpngpolyclippolynompurrrquantregR6raggrbibutilsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRdpackreformulasreshape2Rhdf5librjsonrlangRProtoBufLibRSpectrarstatixrsvdRtsneS4ArraysS4VectorssandwichScaledMatrixscalesscaterscuttleshapeSingleCellExperimentsitmosnowSparseArraySparseMspatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttweenrUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXMLXVectorzoo

spillR Vignette

Marco Guazzini, Alexander G. Reisach, Sebastian Weichwald, Christof Seiler

Rendered fromspillR-vignette.Rmdusingknitr::rmarkdownon Feb 28 2025.

Last update: 2024-03-18
Started: 2023-06-15