Package: CATALYST 1.31.0
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:
CATALYST_1.31.0.tar.gz
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CATALYST_1.31.0.tgz(r-4.4-any)CATALYST_1.29.1.tgz(r-4.3-any)
CATALYST_1.31.0.tar.gz(r-4.5-noble)CATALYST_1.31.0.tar.gz(r-4.4-noble)
CATALYST_1.31.0.tgz(r-4.4-emscripten)CATALYST_1.29.1.tgz(r-4.3-emscripten)
CATALYST.pdf |CATALYST.html✨
CATALYST/json (API)
NEWS
| # 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
- PBMC_fs - Example data sets
- PBMC_md - Example data sets
- PBMC_panel - Example data sets
- isotope_list - Example data sets
- merging_table - Example data sets
- mp_cells - Example data sets
- raw_data - Example data sets
- sample_ff - Example data sets
- sample_key - Example data sets
- ss_exp - Example data sets
On BioConductor:CATALYST-1.31.0(bioc 3.21)CATALYST-1.30.0(bioc 3.20)
clusteringdataimportdifferentialexpressionexperimentaldesignflowcytometryimmunooncologymassspectrometrynormalizationpreprocessingsinglecellsoftwarestatisticalmethodvisualization
Last updated 23 days agofrom:018fa08e60. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | NOTE | Nov 19 2024 |
| R-4.5-linux | NOTE | Nov 19 2024 |
| R-4.4-win | NOTE | Nov 19 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | ERROR | Sep 26 2024 |
| R-4.3-mac | ERROR | Sep 26 2024 |
Exports:adaptSpillmatapplyCutoffsassignPrelimchannelsclrDRclustercluster_codescluster_idscompCytofcomputeSpillmatdelta_areaeiestCutoffsextractClustersfilterSCEguessPanelmarker_classesmergeClustersn_cellsnormCytofpbMDSplotAbundancesplotClusterExprsplotCodesplotCountsplotDiffHeatmapplotDRplotEventsplotExprHeatmapplotExprsplotFreqHeatmapplotMahalplotMultiHeatmapplotNRSplotPbExprsplotScatterplotSpillmatplotYieldsprepDatarunDRsample_idssce2fcsstate_markerstype_markers
Dependencies:abindALLaskpassassortheadbackportsbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbootbroomCairocarcarDatacirclizecliclueclustercodetoolscolorRampscolorspaceComplexHeatmapConsensusClusterPluscorrplotcowplotcpp11crayoncurlcytolibdata.tableDelayedArrayDerivdigestdoBydoParalleldplyrdqrngdrcfansifarverflowCoreFlowSOMFNNforeachformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggforceggnewscaleggplot2ggpubrggrastrggrepelggridgesggsciggsignifGlobalOptionsgluegridExtragtablegtoolshttrigraphIRangesirlbaisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnnlsnumDerivopensslpbkrtestpheatmappillarpkgconfigplotrixplyrpngpolyclippolynompurrrquantregR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressreshape2Rhdf5librjsonrlangRProtoBufLibRSpectrarstatixrsvdRtsneS4ArraysS4VectorssandwichScaledMatrixscalesscaterscuttleshapeSingleCellExperimentsitmosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttweenrUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXMLXVectorzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adapt spillover matrix | adaptSpillmat |
| Single-cell debarcoding (2) | applyCutoffs |
| Single-cell debarcoding (1) | assignPrelim |
| DR plot on CLR of proportions | clrDR |
| 'FlowSOM' clustering & 'ConsensusClusterPlus' metaclustering | cluster |
| Compensate CyTOF data | compCytof |
| Compute spillover matrix | computeSpillmat |
| Example data sets | data isotope_list merging_table mp_cells PBMC_fs PBMC_md PBMC_panel raw_data sample_ff sample_key ss_exp |
| Estimation of distance separation cutoffs | estCutoffs |
| Extract clusters from a 'SingleCellExperiment' | extractClusters |
| 'SingleCellExperiment' filtering | filterSCE |
| Guess parameter panel | guessPanel |
| Manual cluster merging | mergeClusters |
| Bead-based normalization | normCytof |
| Pseudobulk-level MDS plot | pbMDS |
| Population frequencies across samples & clusters | plotAbundances |
| Plot expression distributions by cluster | plotClusterExprs |
| tSNE and PCA on SOM codes | plotCodes |
| Plot cell counts | plotCounts |
| Plot differential heatmap | plotDiffHeatmap |
| Plot reduced dimensions | plotDR |
| Event plot | plotEvents |
| Plot expression heatmap | plotExprHeatmap |
| Expression densities | plotExprs |
| Cluster frequency heatmap | plotFreqHeatmap |
| Biaxial plot | plotMahal |
| Multi-panel expression & frequency heatmaps | plotMultiHeatmap |
| Plot non-redundancy scores | plotNRS |
| Pseudobulk-level boxplot | plotPbExprs |
| Scatter plot | plotScatter |
| Spillover matrix heatmap | plotSpillmat |
| Yield plot | plotYields |
| Data preparation | prepData |
| Dimension reduction | runDR |
| 'SingleCellExperiment' accessors | channels 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 |
