Introduction | Installation | Load PWM annotation | Loading kinase PWMs | Processing user-provided phosphosites | Scoring of user-provided phosphosites | Session info | References
Package: JohnsonKinaseData 1.9.0
Florian Geier
JohnsonKinaseData: Kinase PWMs based on data published by Johnson et al. 2023 and Yaron-Barir et al. 2024
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").
Authors:
JohnsonKinaseData_1.9.0.tar.gz
JohnsonKinaseData_1.9.0.tar.gz(r-4.7-any)JohnsonKinaseData_1.9.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
JohnsonKinaseData/json (API)
| # Install 'JohnsonKinaseData' in R: |
| install.packages('JohnsonKinaseData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fgeier/johnsonkinasedata/issues
On BioConductor:JohnsonKinaseData-1.9.0(data/experiment 3.24)JohnsonKinaseData-1.8.0(data/experiment 3.23)
experimenthubhomo_sapiens_dataproteomedatapkg
Last updated from:2675c64c97. Checks:3 NOTE, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 135 | ||
| linux-devel | NOTE | 326 | ||
| source / vignettes | OK | 350 | ||
| linux-release | NOTE | 414 |
Exports:.JohnsonKinaseAnnotation.JohnsonKinaseBackgroundQuantiles.JohnsonKinaseBackgroundScores.JohnsonKinasePWM.TyrosineKinaseAnnotation.TyrosineKinaseBackgroundQuantiles.TyrosineKinaseBackgroundScores.TyrosineKinasePWMgetBackgroundScoresgetKinaseAnnotationgetKinasePWMgetScoreMapsprocessPhosphopeptidesscorePhosphosites
Dependencies:AnnotationDbiAnnotationHubaskpassbackportsBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobcachemcheckmateclicodetoolscpp11crayoncurlDBIdbplyrdplyrExperimentHubfastmapfilelockformatRfutile.loggerfutile.optionsgenericsgluehttrhttr2IRangesjsonliteKEGGRESTlambda.rlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfosnowstringistringrsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get precomputed PWM scores for two sets of curated human phosphosites | getBackgroundScores |
| Get annnotation data for all kinase PWMs | getKinaseAnnotation |
| Get a list of position specific weight matrices (PWMs) for human kinases | getKinasePWM |
| Map log2-odds score to percentile rank | getScoreMaps |
| processPhosphopetides | processPhosphopeptides |
| Match kinase PWMs to processed phosphosites | scorePhosphosites |