JohnsonKinaseData
Kinase PWMs based on data published by Johnson et al. 2023 (doi:10.1038/s41586-022-05575-3)
Bioconductor version: Release (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 | |
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 |