Package: cytofQC 2.1.0

Jill Lundell

cytofQC: Labels normalized cells for CyTOF data and assigns probabilities for each label

cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.

Authors:Jill Lundell [aut, cre], Kelly Street [aut]

cytofQC_2.1.0.tar.gz
cytofQC_2.1.0.zip(r-4.7)cytofQC_2.1.0.zip(r-4.6)cytofQC_2.1.0.zip(r-4.5)
cytofQC_2.1.0.tgz(r-4.6-any)cytofQC_2.1.0.tgz(r-4.5-any)
cytofQC_2.1.0.tar.gz(r-4.7-any)cytofQC_2.1.0.tar.gz(r-4.6-any)
cytofQC_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cytofQC/json (API)
NEWS

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

Bug tracker:https://github.com/jillbo1000/cytofqc/issues

On BioConductor:cytofQC-2.1.0(bioc 3.24)cytofQC-2.0.0(bioc 3.23)

softwaresinglecellannotation

4.60 score 2 stars 4 scripts 293 downloads 20 exports 227 dependencies

Last updated from:4b960d52e5. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE238
linux-devel-x86_64NOTE498
source / vignettesOK1281
linux-release-x86_64NOTE477
macos-release-arm64NOTE306
macos-oldrel-arm64NOTE229
windows-develNOTE392
windows-releaseNOTE395
windows-oldrelNOTE388
wasm-releaseOK231

Exports:cytofHistcytofQCreportgbmLabelinitialinitialBeadinitialDeadinitialDebrisinitialDoubletinitialGuesslabellabelQCmodelDataplotInitialGuessprobsreadCytofrfLabels3vmLabelscoressvmLabeltech

Dependencies:abindadaALLaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocGenericsbiocmakeBiocManagerBiocNeighborsBiocParallelBiocSingularBiocStylebitopsbookdownbootbroombslibcachemCairocarcarDataCATALYSTcaToolscirclizeclasscliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncrosstalkcurlcytolibdata.tableDelayedArrayDerivdigestdir.expirydoBydoParalleldplyrdqrngdrce1071evaluateEZtunefarverfastmapfilelockflowCoreFlowSOMFNNfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsGAgbmgenericsGenomicRangesGetoptLongggbeeswarmggforceggnewscaleggplot2ggpubrggrastrggrepelggridgesggsciggsignifglmnetGlobalOptionsgluegplotsgridExtragtablegtoolshighrhtmltoolshtmlwidgetshttrigraphIRangesirlbaisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamixtoolsmodelrmultcompmvtnormnlmenloptrnnetnnlsnumDerivopenssloptimxotelpbkrtestpheatmappillarpkgconfigplotlyplotrixplyrpngpolyclippolynompracmapromisesproxypurrrquantregR6raggrandomForestrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRdpackreformulasreshape2Rhdf5librjsonrlangrmarkdownROCRrpartRProtoBufLibRSpectrarstatixrsvdRtsneS4ArraysS4VectorsS7sandwichsassScaledMatrixscalesscaterscuttlesegmentedSeqinfoshapeSingleCellExperimentsitmosnowSparseArraySparseMsscstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttimeDatetinytextweenrurcautf8uwotvctrsviporviridisviridisLitewithrxfunXMLXVectoryamlzoo

Complete Guide to cytofQC

Rendered fromcytofQC.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-01-11
Started: 2022-10-07