Package: CATALYST 1.37.0

Helena L. Crowell

CATALYST: Cytometry dATa anALYSis Tools

CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.

Authors:Helena L. Crowell [aut, cre], Vito R.T. Zanotelli [aut], Stéphane Chevrier [aut, dtc], Mark D. Robinson [aut, fnd], Bernd Bodenmiller [fnd]

CATALYST_1.37.0.tar.gz
CATALYST_1.37.0.zip(r-4.7)CATALYST_1.37.0.zip(r-4.6)CATALYST_1.37.0.zip(r-4.5)
CATALYST_1.37.0.tgz(r-4.6-any)CATALYST_1.37.0.tgz(r-4.5-any)
CATALYST_1.37.0.tar.gz(r-4.7-any)CATALYST_1.37.0.tar.gz(r-4.6-any)
CATALYST_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CATALYST/json (API)

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

Bug tracker:https://github.com/helenalc/catalyst/issues

Datasets:

On BioConductor:CATALYST-1.37.0(bioc 3.24)CATALYST-1.36.0(bioc 3.23)

clusteringdataimportdifferentialexpressionexperimentaldesignflowcytometryimmunooncologymassspectrometrynormalizationpreprocessingsinglecellsoftwarestatisticalmethodvisualization

11.50 score 75 stars 3 packages 964 scripts 37 mentions 44 exports 166 dependencies

Last updated from:4740c0e4b1. Checks:6 NOTE, 2 ERROR, 2 OK. Indexed: yes.

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bioc-checksNOTE243
linux-devel-x86_64ERROR674
source / vignettesOK400
linux-release-x86_64NOTE711
macos-release-arm64NOTE328
macos-oldrel-arm64NOTE286
windows-develERROR576
windows-releaseNOTE539
windows-oldrelNOTE543
wasm-releaseOK235

Exports:adaptSpillmatapplyCutoffsassignPrelimchannelsclrDRclustercluster_codescluster_idscompCytofcomputeSpillmatdelta_areaeiestCutoffsextractClustersfilterSCEguessPanelmarker_classesmergeClustersn_cellsnormCytofpbMDSplotAbundancesplotClusterExprsplotCodesplotCountsplotDiffHeatmapplotDRplotEventsplotExprHeatmapplotExprsplotFreqHeatmapplotMahalplotMultiHeatmapplotNRSplotPbExprsplotScatterplotSpillmatplotYieldsprepDatarunDRsample_idssce2fcsstate_markerstype_markers

Dependencies:abindALLassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocGenericsbiocmakeBiocNeighborsBiocParallelBiocSingularbootbroomcarcarDatacirclizecliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncytolibDelayedArrayDerivdigestdir.expirydoBydoParalleldplyrdqrngdrcfarverfilelockflowCoreFlowSOMFNNforeachforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggbeeswarmggforceggnewscaleggplot2ggpubrggrepelggridgesggsciggsignifGlobalOptionsgluegridExtragtablegtoolsigraphIRangesirlbaisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvminqamodelrmultcompmvtnormnlmenloptrnnetnnlsnumDerivpbkrtestpheatmappillarpkgconfigplotrixplyrpngpolyclippolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRdpackreformulasreshape2Rhdf5librjsonrlangRProtoBufLibRSpectrarstatixrsvdRtsneS4ArraysS4VectorsS7sandwichScaledMatrixscalesscaterscuttleSeqinfoshapeSingleCellExperimentsitmosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystemfontsTH.datatibbletidyrtidyselecttimeDatetweenrurcautf8uwotvctrsviporviridisviridisLitewithrXMLXVectorzoo

Preprocessing with CATALYST
Data examples | Data organization | Normalization | Normalization workflow | normCytof: Normalization using bead standards | Debarcoding | Debarcoding workflow | assignPrelim: Assignment of preliminary IDs | estCutoffs: Estimation of separation cutoffs | plotYields: Selecting barcode separation cutoffs | applyCutoffs: Applying deconvolution parameters | plotEvents: Normalized intensities | plotMahal: All barcode biaxial plot | Compensation | Compensation workflow | computeSpillmat: Estimation of the spillover matrix | plotSpillmat: Spillover matrix heatmap | compCytof: Compensation of mass cytometry data | Scatter plot visualization | Example 1: Coloring by cell density | Example 2: Coloring by variables | Example 3: Facetting by variables | Conversion to other data structures | Writing FCS files | Gating & visualization | Session information | References
Rendered frompreprocessing.Rmdusingknitr::rmarkdown

Last update: 2025-10-05
Started: 2018-05-13

Differential discovery with CATALYST
Example data | Data preparation | Clustering | cluster: FlowSOM clustering & ConsensusClusterPlus metaclustering | mergeClusters: Manual cluster merging | Delta area plot | Visualization | plotCounts: Number of cells measured per sample | pbMDS: Pseudobulk-level MDS plot | Ex. 2: MDS on sample-level pseudobulks | Ex. 1: MDS on pseudobulks by cluster-sample | clrDR: Reduced dimension plot on CLR of proportions | Ex. 1: CLR on cluster proportions across samples | Ex. 2: CLR on sample proportions across clusters | plotExprHeatmap: Heatmap of aggregated marker expressions | plotPbExprs: Pseudobulk expression boxplot | plotClusterExprs: Marker-densities by cluster | plotAbundances: Relative population abundances | plotFreqHeatmap: Heatmap of cluster fequencies | plotMultiHeatmap: Multi-panel Heatmaps | Ex. 1: Type- & state-markers | Ex. 2: CDx markers & cluster frequencies | Ex. 3: Selected markers | Dimensionality reduction | Filtering | Differental testing with r BiocStyle::Biocpkg("diffcyt") | plotDiffHeatmap: Heatmap of differential testing results | Ex. 1: DA testing results | Ex. 2: DS testing results | Ex. 3: Filtering results | Ex. 4: Customizing appearance | More | Exporting FCS files | Using other clustering algorithms | Customizing visualizations | Modifying ggplots | Modifying ComplexHeatmaps | Combining ComplexHeatmaps | Ex. 1: type- & state-markers + cluster frequencies | Ex. 2: frequencies + selected markers + all markers | Session information | References
Rendered fromdifferential.Rmdusingknitr::rmarkdown

Last update: 2025-10-05
Started: 2020-04-14

Readme and manuals

Help Manual

Help pageTopics
Adapt spillover matrixadaptSpillmat
Single-cell debarcoding (2)applyCutoffs
Single-cell debarcoding (1)assignPrelim
DR plot on CLR of proportionsclrDR
'FlowSOM' clustering & 'ConsensusClusterPlus' metaclusteringcluster
Compensate CyTOF datacompCytof
Compute spillover matrixcomputeSpillmat
Example data setsdata isotope_list merging_table mp_cells PBMC_fs PBMC_md PBMC_panel raw_data sample_ff sample_key ss_exp
Estimation of distance separation cutoffsestCutoffs
Extract clusters from a 'SingleCellExperiment'extractClusters
'SingleCellExperiment' filteringfilterSCE
Guess parameter panelguessPanel
Manual cluster mergingmergeClusters
Bead-based normalizationnormCytof
Pseudobulk-level MDS plotpbMDS
Population frequencies across samples & clustersplotAbundances
Plot expression distributions by clusterplotClusterExprs
tSNE and PCA on SOM codesplotCodes
Plot cell countsplotCounts
Plot differential heatmapplotDiffHeatmap
Plot reduced dimensionsplotDR
Event plotplotEvents
Plot expression heatmapplotExprHeatmap
Expression densitiesplotExprs
Cluster frequency heatmapplotFreqHeatmap
Biaxial plotplotMahal
Multi-panel expression & frequency heatmapsplotMultiHeatmap
Plot non-redundancy scoresplotNRS
Pseudobulk-level boxplotplotPbExprs
Scatter plotplotScatter
Spillover matrix heatmapplotSpillmat
Yield plotplotYields
Data preparationprepData
Dimension reductionrunDR
'SingleCellExperiment' accessorschannels channels,SingleCellExperiment-method cluster_codes cluster_codes,SingleCellExperiment-method cluster_ids cluster_ids,SingleCellExperiment,character-method cluster_ids,SingleCellExperiment,missing-method delta_area delta_area,SingleCellExperiment-method ei ei,SingleCellExperiment-method marker_classes marker_classes,SingleCellExperiment-method n_cells n_cells,SingleCellExperiment-method sample_ids sample_ids,SingleCellExperiment-method SCE-accessors state_markers state_markers,SingleCellExperiment-method type_markers type_markers,SingleCellExperiment-method
SCE to 'flowFrame/Set'sce2fcs