Package: diffcyt 1.31.0
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:
diffcyt_1.31.0.tar.gz
diffcyt_1.31.0.zip(r-4.6)diffcyt_1.31.0.zip(r-4.5)diffcyt_1.31.0.zip(r-4.4)
diffcyt_1.31.0.tgz(r-4.5-any)
diffcyt_1.31.0.tar.gz(r-4.6-any)diffcyt_1.31.0.tar.gz(r-4.5-any)
diffcyt_1.31.0.tgz(r-4.5-emscripten)
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-1.31.0(bioc 3.23)diffcyt-1.30.0(bioc 3.22)
immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware
Last updated from:5b52099474. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Total time | Artifact |
|---|---|---|---|
| bioc-checks | ERROR | 239 | |
| linux-devel-x86_64 | NOTE | 390 | |
| source / vignettes | OK | 422 | |
| linux-release-x86_64 | NOTE | 385 | |
| macos-release-arm64 | NOTE | 238 | |
| macos-oldrel-arm64 | NOTE | 340 | |
| windows-devel | NOTE | 312 | |
| windows-release | NOTE | 329 | |
| windows-oldrel | NOTE | 331 | |
| wasm-release | OK | 230 |
Exports:calcCountscalcMedianscalcMediansByClusterMarkercalcMediansBySampleMarkercreateContrastcreateDesignMatrixcreateFormuladiffcytgenerateClustersplotHeatmapprepareDatatestDA_edgeRtestDA_GLMMtestDA_voomtestDS_limmatestDS_LMMtopClusterstopTabletransformData
Dependencies:abindALLbackportsbase64encBHBiobaseBiocGenericsbootbroomcarcarDatacirclizecliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncytolibDelayedArrayDerivdigestdoBydoParalleldplyredgeRfarverflowCoreFlowSOMforeachFormulagenericsGenomicRangesGetoptLongggforceggnewscaleggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtableigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkminqamodelrmultcompmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpngpolyclippolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasreshape2Rhdf5librjsonrlangRProtoBufLibrstatixRtsneS4ArraysS4VectorsS7sandwichscalesSeqinfoshapeSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystemfontsTH.datatibbletidyrtidyselecttweenrutf8vctrsviridisLitewithrXMLXVectorzoo
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 |
