Package: cytoKernel 1.11.0

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:Tusharkanti Ghosh [aut, cre], Victor Lui [aut], Pratyaydipta Rudra [aut], Souvik Seal [aut], Thao Vu [aut], Elena Hsieh [aut], Debashis Ghosh [aut, cph]

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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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

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-1.11.0(bioc 3.20)cytoKernel-1.10.0(bioc 3.19)

bioconductor-package

10 exports 0.49 score 77 dependencies

Last updated 2 months agofrom:52a4864285

Exports:CytoK CytoKalpha CytoKData CytoKDEData CytoKDEfeatures CytoKFeatures CytoKFeaturesOrdered CytoKFeatureVars CytoKProc plotCytoK

Dependencies:abind ashr askpass BH Biobase BiocGenerics BiocParallel circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DelayedArray digest doParallel dplyr etrunct fansi foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong GlobalOptions glue httr invgamma IRanges irlba iterators jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime mixsqp openssl pillar pkgconfig png R6 RColorBrewer Rcpp RcppArmadillo rjson rlang S4Arrays S4Vectors shape snow SparseArray SQUAREM SummarizedExperiment sys tibble tidyselect truncnorm UCSC.utils utf8 vctrs withr XVector zlibbioc

The cytoKernel user's guide

Tusharkanti Ghosh, Victor Lui, Pratyaydipta Rudra, Souvik Seal, Thao Vu, Elena Hsieh, Debashis Ghosh

Rendered fromcytoKernel.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-10-01
Started: 2021-10-01

Help page	Topics
Example of processed dimensionally reduced flow cytometry (marker median intensities) Bodenmiller_BCR_XL_flowSet() expression dataset from HDCytoData Bioconductor data package.	cytoHDBMW
CytoK	CytoK
the CytoK class	CytoK-class
Generic function that returns the CytoK level of significance (alpha) Given a CytoK object, this function returns the CytoK alpha	CytoKalpha CytoKalpha,CytoK-method
Generic function that returns the CytoK Data	CytoKData CytoKData,CytoK-method
Differentially expressed data by cytoKernel	CytoKDEData
Generic function that returns the CytoK Differentially Expressed (DE) features Given a CytoK object, this function returns the CytoK DE features	CytoKDEfeatures CytoKDEfeatures,CytoK-method
Generic function that returns the CytoK features	CytoKFeatures CytoKFeatures,CytoK-method
Generic function that returns the ordered CytoK features	CytoKFeaturesOrdered CytoKFeaturesOrdered,CytoK-method
Generic function that returns the CytoK Feature Vars	CytoKFeatureVars CytoKFeatureVars,CytoK-method
CytoKProc	CytoKProc
S4 Class union	data.frameORSummarizedExperiment-class
Heatmap of the differentially expressed data with features on the rows and samples (group factors) as the columns from 'CytoK' and 'CytoKDEData' function.	plotCytoK
S4 Class union	vectorORNull-class

Package: cytoKernel 1.11.0

cytoKernel: Differential expression using kernel-based score test

The cytoKernel user's guide

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