Introduction to KinSwing | KinSwingR example workflow | Extracting peptides for analysis | Build Position Weight Matrices (PWMs) | Visualising motifs | Score PWM matches against peptide sequences | Predict kinase activity using swing() | KinSwingR algorithm | References
Package: KinSwingR 1.31.0
Ashley J. Waardenberg
KinSwingR: KinSwingR: network-based kinase activity prediction
KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity.
Authors:
KinSwingR_1.31.0.tar.gz
KinSwingR_1.31.0.zip(r-4.7)KinSwingR_1.31.0.zip(r-4.6)KinSwingR_1.31.0.zip(r-4.5)
KinSwingR_1.31.0.tgz(r-4.6-any)KinSwingR_1.31.0.tgz(r-4.5-any)
KinSwingR_1.31.0.tar.gz(r-4.7-any)KinSwingR_1.31.0.tar.gz(r-4.6-any)
KinSwingR_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
KinSwingR/json (API)
| # Install 'KinSwingR' in R: |
| install.packages('KinSwingR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- example_phosphoproteome - Example phosphoproteome.
- phosphositeplus_human - Human kinase-substrates derived from PhosphositePlus.
On BioConductor:KinSwingR-1.31.0(bioc 3.24)KinSwingR-1.30.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
proteomicssequencematchingnetwork
Last updated from:b1c20f9c17. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 144 | ||
| linux-devel-x86_64 | OK | 216 | ||
| source / vignettes | OK | 217 | ||
| linux-release-x86_64 | OK | 262 | ||
| macos-release-arm64 | OK | 121 | ||
| macos-oldrel-arm64 | OK | 115 | ||
| windows-devel | OK | 106 | ||
| windows-release | OK | 139 | ||
| windows-oldrel | OK | 118 | ||
| wasm-release | OK | 115 |
Exports:buildPWMcleanAnnotationscoreSequencesswingviewPWM
Dependencies:BHBiocParallelbitbit64blobcachemchronclicodetoolscpp11data.tableDBIfastmapformatRfutile.loggerfutile.optionsgluegsubfnlambda.rlifecyclememoisepkgconfigprotorlangRSQLitesnowsqldfvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Generate Position Weight Matrices (PWMs) | buildPWM |
| Function for extracting peptide sequences from multimapped or complex annotated data | cleanAnnotation |
| Example phosphoproteome. | example_phosphoproteome |
| KinSwingR: A package for predicting kinase activity | KinSwingR-package KinSwingR |
| Human kinase-substrates derived from PhosphositePlus. | phosphositeplus_human |
| Score substrate sequences for matches to kinase Position Weight Matrices (PWMs) | scoreSequences |
| Swing statistic | swing |
| View motif | viewPWM |
