Package: diffcyt 1.32.0

Lukas M. Weber

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.

Authors:Lukas M. Weber [aut, cre]

diffcyt_1.32.0.tar.gz
diffcyt_1.32.0.zip(r-4.7)diffcyt_1.32.0.zip(r-4.6)diffcyt_1.32.0.zip(r-4.5)
diffcyt_1.32.0.tgz(r-4.6-any)diffcyt_1.32.0.tgz(r-4.5-any)
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diffcyt_1.32.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
diffcyt/json (API)
NEWS

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

Bug tracker:https://github.com/lmweber/diffcyt/issues

On BioConductor:diffcyt-1.33.0(bioc 3.24)diffcyt-1.32.0(bioc 3.23)

immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware

8.85 score 25 stars 5 packages 272 scripts 930 downloads 18 mentions 19 exports 137 dependencies

Last updated from:6866188988 (on RELEASE_3_23). Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING257
linux-devel-x86_64WARNING490
source / vignettesERROR404
linux-release-x86_64WARNING501
macos-release-arm64WARNING326
macos-oldrel-arm64WARNING250
windows-develWARNING549
windows-releaseWARNING644
windows-oldrelWARNING638
wasm-releaseOK235

Exports:calcCountscalcMedianscalcMediansByClusterMarkercalcMediansBySampleMarkercreateContrastcreateDesignMatrixcreateFormuladiffcytgenerateClustersplotHeatmapprepareDatatestDA_edgeRtestDA_GLMMtestDA_voomtestDS_limmatestDS_LMMtopClusterstopTabletransformData

Dependencies:abindALLbackportsbase64encBHBiobaseBiocGenericsbiocmakebootbroomcarcarDatacirclizecliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncytolibDelayedArrayDerivdigestdir.expirydoBydoParalleldplyredgeRfarverfilelockflowCoreFlowSOMforeachforecastFormulafracdiffgenericsGenomicRangesGetoptLongggforceggnewscaleggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtableigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrmultcompmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpngpolyclippolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2Rhdf5librjsonrlangRProtoBufLibrstatixRtsneS4ArraysS4VectorsS7sandwichscalesSeqinfoshapeSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystemfontsTH.datatibbletidyrtidyselecttimeDatetweenrurcautf8vctrsviridisLitewithrXMLXVectorzoo