Package: cytoKernel 1.13.0
Tusharkanti Ghosh
cytoKernel: Differential expression using kernel-based score test
cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression data. In this R package, we implement functions that compute the feature-wise p values and their corresponding adjusted p values. Additionally, it also computes the feature-wise shrunk effect sizes and their corresponding shrunken effect size. Further, it calculates the percent of differentially expressed features and plots user-friendly heatmap of the top differentially expressed features on the rows and samples on the columns.
Authors:
cytoKernel_1.13.0.tar.gz
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cytoKernel.pdf |cytoKernel.html✨
cytoKernel/json (API)
NEWS
# Install 'cytoKernel' in R: |
install.packages('cytoKernel', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ghoshlab/cytokernel/issues
- cytoHDBMW - Example of processed dimensionally reduced flow cytometry (marker median intensities) Bodenmiller_BCR_XL_flowSet() expression dataset from HDCytoData Bioconductor data package.
On BioConductor:cytoKernel-1.13.0(bioc 3.21)cytoKernel-1.12.0(bioc 3.20)
immunooncologyproteomicssinglecellsoftwareonechannelflowcytometrydifferentialexpressiongeneexpressionclusteringcpp
Last updated 2 months agofrom:ee6062c066. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 18 2024 |
R-4.5-win-x86_64 | OK | Dec 18 2024 |
R-4.5-linux-x86_64 | OK | Dec 18 2024 |
R-4.4-win-x86_64 | OK | Dec 18 2024 |
R-4.4-mac-x86_64 | OK | Dec 18 2024 |
R-4.4-mac-aarch64 | OK | Dec 18 2024 |
R-4.3-win-x86_64 | OK | Dec 18 2024 |
R-4.3-mac-x86_64 | OK | Dec 18 2024 |
R-4.3-mac-aarch64 | OK | Dec 18 2024 |
Exports:CytoKCytoKalphaCytoKDataCytoKDEDataCytoKDEfeaturesCytoKFeaturesCytoKFeaturesOrderedCytoKFeatureVarsCytoKProcplotCytoK
Dependencies:abindashraskpassBHBiobaseBiocGenericsBiocParallelcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDelayedArraydigestdoParalleldplyretrunctfansiforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongGlobalOptionsgluehttrinvgammaIRangesirlbaiteratorsjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimemixsqpopensslpillarpkgconfigpngR6RColorBrewerRcppRcppArmadillorjsonrlangS4ArraysS4VectorsshapesnowSparseArraySQUAREMSummarizedExperimentsystibbletidyselecttruncnormUCSC.utilsutf8vctrswithrXVectorzlibbioc