JohnsonKinaseData
This is the released version of JohnsonKinaseData; for the devel version, see JohnsonKinaseData.
Kinase PWMs based on data published by Johnson et al. 2023 and Yaron-Barir et al. 2024
Bioconductor version: Release (3.23)
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]
Maintainer: Florian Geier <florian.geier at unibas.ch>
citation("JohnsonKinaseData")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.8.0 |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |