Package: diffcyt 1.27.3
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:
diffcyt_1.27.3.tar.gz
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diffcyt.pdf |diffcyt.html✨
diffcyt/json (API)
NEWS
| # Install 'diffcyt' in R: |
| install.packages('diffcyt', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lmweber/diffcyt/issues
On BioConductor:diffcyt-1.27.0(bioc 3.21)diffcyt-1.26.0(bioc 3.20)
immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware
Last updated 26 days agofrom:a4da91421b. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 10 2025 |
| R-4.5-win | NOTE | Feb 10 2025 |
| R-4.5-mac | WARNING | Feb 10 2025 |
| R-4.5-linux | NOTE | Feb 10 2025 |
| R-4.4-win | NOTE | Feb 10 2025 |
| R-4.4-mac | NOTE | Feb 10 2025 |
| R-4.3-win | NOTE | Feb 10 2025 |
| R-4.3-mac | NOTE | Feb 10 2025 |
Exports:calcCountscalcMedianscalcMediansByClusterMarkercalcMediansBySampleMarkercreateContrastcreateDesignMatrixcreateFormuladiffcytgenerateClustersplotHeatmapprepareDatatestDA_edgeRtestDA_GLMMtestDA_voomtestDS_limmatestDS_LMMtopClusterstopTabletransformData
Dependencies:abindALLaskpassbackportsBHBiobaseBiocGenericsbootbroomcarcarDatacirclizecliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncurlcytolibDelayedArrayDerivdigestdoBydoParalleldplyredgeRfansifarverflowCoreFlowSOMforeachFormulagenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggforceggnewscaleggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpngpolyclippolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2Rhdf5librjsonrlangRProtoBufLibrstatixRtsneS4ArraysS4VectorssandwichscalesshapeSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontsTH.datatibbletidyrtidyselecttweenrUCSC.utilsutf8vctrsviridisLitewithrXMLXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate cluster cell counts | calcCounts |
| Calculate cluster medians | calcMedians |
| Calculate medians (by cluster and marker) | calcMediansByClusterMarker |
| Calculate medians (by sample and marker) | calcMediansBySampleMarker |
| Create contrast matrix | createContrast |
| Create design matrix | createDesignMatrix |
| Create model formula and corresponding data frame of variables | createFormula |
| Run 'diffcyt' pipeline | diffcyt-package diffcyt |
| Generate clusters | generateClusters |
| Plot heatmap | plotHeatmap |
| Prepare data | prepareData |
| Test for differential abundance: method 'diffcyt-DA-edgeR' | testDA_edgeR |
| Test for differential abundance: method 'diffcyt-DA-GLMM' | testDA_GLMM |
| Test for differential abundance: method 'diffcyt-DA-voom' | testDA_voom |
| Test for differential states: method 'diffcyt-DS-limma' | testDS_limma |
| Test for differential states: method 'diffcyt-DS-LMM' | testDS_LMM |
| Alias for 'topTable' (deprecated) | topClusters |
| Show table of results for top clusters or cluster-marker combinations | topTable |
| Transform data | transformData |
