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JohnsonKinaseData

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 (doi:10.1038/s41586-022-05575-3)


Bioconductor version: Development (3.20)

The packages provides position specific weight matrices (PWMs) for 303 human serine/threonine kinases originally published in Johnson et al. 2023. It includes gene annotation for each kinase PWM and PWM matching scores for a set of 85603 curated human phosphosites which can be used to map a PWM score to its percentile rank. The package also includes basic functionality to score user provided phosphosites.

Author: Florian Geier [aut, cre]

Maintainer: Florian Geier <florian.geier at unibas.ch>

Citation (from within R, enter citation("JohnsonKinaseData")):

Installation

To install this package, start R (version "4.4") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("JohnsonKinaseData")
JohnsonKinaseData HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, Proteome
Version 1.1.0
License MIT + file LICENSE
Depends
Imports ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr, tidyr, purrr, utils
System Requirements
URL https://github.com/fgeier/JohnsonKinaseData/
Bug Reports https://support.bioconductor.org/t/JohnsonKinaseData
See More
Suggests knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0), rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package JohnsonKinaseData_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/JohnsonKinaseData
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/JohnsonKinaseData
Package Short Url https://bioconductor.org/packages/JohnsonKinaseData/
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