JohnsonKinaseData
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see JohnsonKinaseData.
Kinase PWMs based on data published by Johnson et al. 2023 (doi:10.1038/s41586-022-05575-3)
Bioconductor version: 3.19
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("JohnsonKinaseData")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, Proteome |
| Version | 1.0.0 |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| 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/ |
| Package Downloads Report | Download Stats |