This is the development version of cytoKernel; for the stable release version, see cytoKernel.
Differential expression using kernel-based score testBioconductor version: Development (3.22)
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.
Author: Tusharkanti Ghosh [aut, cre], Victor Lui [aut], Pratyaydipta Rudra [aut], Souvik Seal [aut], Thao Vu [aut], Elena Hsieh [aut], Debashis Ghosh [aut, cph]
Maintainer: Tusharkanti Ghosh <tusharkantighosh30 at gmail.com>
Citation (from within R, entercitation("cytoKernel")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("cytoKernel")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cytoKernel")Follow Installation instructions to use this package in your R session.
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