Introduction | Overview of 'diffcyt' methodology | Summary | Differential abundance (DA) and differential states (DS) | Flexible experimental designs and contrasts | More details | Installation | 'diffcyt' pipeline | Dataset | Load data from 'HDCytoData' package | Alternatively: load data from '.fcs' files | Set up meta-data | Set up design matrix (or model formula) | Set up contrast matrix | Differential testing | Option 1: Wrapper function using input data from '.fcs' files | Option 2: Wrapper function using CATALYST 'daFrame' object | Option 3: Individual functions | Prepare data into required format | Transform data | Generate clusters | Calculate features | Test for differential abundance (DA) of cell populations | Test for differential states (DS) within cell populations | Exporting data | Visualizations using 'CATALYST' package | Overview | Heatmap: DA test results | Heatmap: DS test results | References
Package: diffcyt 1.33.0
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_1.33.0.tar.gz
diffcyt_1.33.0.zip(r-4.7)diffcyt_1.33.0.zip(r-4.6)diffcyt_1.33.0.zip(r-4.5)
diffcyt_1.33.0.tgz(r-4.6-any)diffcyt_1.33.0.tgz(r-4.5-any)
diffcyt_1.33.0.tar.gz(r-4.7-any)diffcyt_1.33.0.tar.gz(r-4.6-any)
diffcyt_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
diffcyt/json (API)
| # 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-1.33.0(bioc 3.24)diffcyt-1.32.0(bioc 3.23)
immunooncologyflowcytometryproteomicssinglecellcellbasedassayscellbiologyclusteringfeatureextractionsoftware
Last updated from:b25e063aad. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 254 | ||
| linux-devel-x86_64 | NOTE | 427 | ||
| source / vignettes | OK | 453 | ||
| linux-release-x86_64 | NOTE | 531 | ||
| macos-release-arm64 | NOTE | 214 | ||
| macos-oldrel-arm64 | NOTE | 202 | ||
| windows-devel | NOTE | 619 | ||
| windows-release | NOTE | 626 | ||
| windows-oldrel | NOTE | 465 | ||
| wasm-release | OK | 258 |
Exports:calcCountscalcMedianscalcMediansByClusterMarkercalcMediansBySampleMarkercreateContrastcreateDesignMatrixcreateFormuladiffcytgenerateClustersplotHeatmapprepareDatatestDA_edgeRtestDA_GLMMtestDA_voomtestDS_limmatestDS_LMMtopClusterstopTabletransformData
Dependencies:abindALLbackportsbase64encBHBiobaseBiocGenericsbiocmakebootbroomcarcarDatacirclizecliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncytolibDelayedArrayDerivdigestdir.expirydoBydoParalleldplyredgeRfarverfilelockflowCoreFlowSOMforeachforecastFormulafracdiffgenericsGenomicRangesGetoptLongggforceggnewscaleggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtableigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvminqamodelrmultcompmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplyrpngpolyclippolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2Rhdf5librjsonrlangRProtoBufLibrstatixRtsneS4ArraysS4VectorsS7sandwichscalesSeqinfoshapeSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystemfontsTH.datatibbletidyrtidyselecttimeDatetweenrurcautf8vctrsviridisLitewithrXMLXVectorzoo
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 |
