Package: cytofQC 1.7.0

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_1.7.0.tar.gz
cytofQC_1.7.0.zip(r-4.5)cytofQC_1.7.0.zip(r-4.4)cytofQC_1.7.0.zip(r-4.3)
cytofQC_1.7.0.tgz(r-4.5-any)cytofQC_1.7.0.tgz(r-4.4-any)cytofQC_1.7.0.tgz(r-4.3-any)
cytofQC_1.7.0.tar.gz(r-4.5-noble)cytofQC_1.7.0.tar.gz(r-4.4-noble)
cytofQC_1.7.0.tgz(r-4.4-emscripten)cytofQC_1.7.0.tgz(r-4.3-emscripten)
cytofQC.pdf |cytofQC.html✨
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-1.7.0(bioc 3.21)cytofQC-1.6.0(bioc 3.20)

softwaresinglecellannotation

4.30 score 2 stars 3 scripts 214 downloads 20 exports 220 dependencies

Last updated 5 months agofrom:c4c778edd4. Checks:3 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winNOTEMar 29 2025
R-4.5-macNOTEMar 29 2025
R-4.5-linuxNOTEMar 29 2025
R-4.4-winNOTEMar 29 2025
R-4.4-macNOTEMar 29 2025
R-4.4-linuxNOTEMar 29 2025
R-4.3-winOKMar 29 2025
R-4.3-macOKMar 29 2025

Exports:cytofHistcytofQCreportgbmLabelinitialinitialBeadinitialDeadinitialDebrisinitialDoubletinitialGuesslabellabelQCmodelDataplotInitialGuessprobsreadCytofrfLabels3vmLabelscoressvmLabeltech

Dependencies:abindadaALLaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocManagerBiocNeighborsBiocParallelBiocSingularBiocStylebitopsbookdownbootbroombslibcachemCairocarcarDataCATALYSTcaToolscirclizeclasscliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncurlcytolibdata.tableDelayedArrayDerivdigestdoBydoParalleldplyrdqrngdrce1071evaluateextrafontextrafontdbEZtunefansifarverfastmapflowCoreFlowSOMFNNfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRFormulafsfutile.loggerfutile.optionsGAgbmgdtoolsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggforceggnewscaleggplot2ggpubrggrastrggrepelggridgesggsciggsignifglmnetGlobalOptionsgluegplotsgridExtragtablegtoolshighrhrbrthemeshtmltoolshttrigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnnlsnumDerivopenssloptimxpbkrtestpheatmappillarpkgconfigplotrixplyrpngpolyclippolynompracmaproxypurrrquantregR6raggrandomForestrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRdpackreformulasreshape2Rhdf5librjsonrlangrmarkdownROCRrpartRProtoBufLibRSpectrarstatixrsvdRtsneRttf2pt1S4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscuttleshapeSingleCellExperimentsitmosnowSparseArraySparseMsscstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttinytextweenrUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXMLXVectoryamlzoo

Complete Guide to cytofQC

Rendered fromcytofQC.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2023-03-15
Started: 2022-10-07