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:
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_1.5.0.tgz(r-4.4-any)cytofQC_1.5.0.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)
Last updated 2 months agofrom:c4c778edd4. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Oct 02 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Oct 02 2024 |
Exports:cytofHistcytofQCreportgbmLabelinitialinitialBeadinitialDeadinitialDebrisinitialDoubletinitialGuesslabellabelQCmodelDataplotInitialGuessprobsreadCytofrfLabels3vmLabelscoressvmLabeltech
Dependencies:abindadaALLaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocManagerBiocNeighborsBiocParallelBiocSingularBiocStylebitopsbookdownbootbroombslibcachemCairocarcarDataCATALYSTcaToolscirclizeclasscliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncurlcytolibdata.tableDelayedArrayDerivdigestdoBydoParalleldplyrdqrngdrce1071evaluateextrafontextrafontdbEZtunefansifarverfastmapflowCoreFlowSOMFNNfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRFormulafsfutile.loggerfutile.optionsGAgbmgdtoolsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggforceggnewscaleggplot2ggpubrggrastrggrepelggridgesggsciggsignifglmnetGlobalOptionsgluegplotsgridExtragtablegtoolshighrhrbrthemeshtmltoolshttrigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnnlsnumDerivopenssloptimxpbkrtestpheatmappillarpkgconfigplotrixplyrpngpolyclippolynompracmaproxypurrrquantregR6raggrandomForestrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressreshape2Rhdf5librjsonrlangrmarkdownROCRrpartRProtoBufLibRSpectrarstatixrsvdRtsneRttf2pt1S4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscuttleshapeSingleCellExperimentsitmosnowSparseArraySparseMsscstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttinytextweenrUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXMLXVectoryamlzlibbioczoo
