This is the development version of JohnsonKinaseData; for the stable release version, see JohnsonKinaseData.
Kinase PWMs based on data published by Johnson et al. 2023 and Yaron-Barir et al. 2024Bioconductor version: Development (3.22)
The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine and 93 tyrosine kinases originally published in Johnson et al. 2023 (doi:10.1038/s41586-022-05575-3) and Yaron-Barir et al. 2024 (doi:10.1038/s41586-024-07407-y). The package includes basic functionality to score user provided phosphosites. It also includes pre-computed PWM scores ("background scores") for a large collection of curated human phosphosites which can be used to rank PWM scores relative to the background scores ("percentile rank").
Author: Florian Geier [aut, cre] ORCID: 0000-0002-9076-9264
Maintainer: Florian Geier <florian.geier at unibas.ch>
Citation (from within R, entercitation("JohnsonKinaseData")): 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("JohnsonKinaseData")
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("JohnsonKinaseData")Follow Installation instructions to use this package in your R session.
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