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 and Yaron-Barir et al. 2024
Bioconductor version: Development (3.21)
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:
Maintainer: Florian Geier <florian.geier at unibas.ch>
citation("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.
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 | 1.3.0 |
| 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_1.3.0.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 |