Package: Path2PPI 1.37.0
Oliver Philipp
Path2PPI: Prediction of pathway-related protein-protein interaction networks
Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.
Authors:
Path2PPI_1.37.0.tar.gz
Path2PPI_1.37.0.zip(r-4.5)Path2PPI_1.37.0.zip(r-4.4)Path2PPI_1.37.0.zip(r-4.3)
Path2PPI_1.37.0.tgz(r-4.4-any)Path2PPI_1.37.0.tgz(r-4.3-any)
Path2PPI_1.37.0.tar.gz(r-4.5-noble)Path2PPI_1.37.0.tar.gz(r-4.4-noble)
Path2PPI_1.37.0.tgz(r-4.4-emscripten)Path2PPI_1.37.0.tgz(r-4.3-emscripten)
Path2PPI.pdf |Path2PPI.html✨
Path2PPI/json (API)
NEWS
| # Install 'Path2PPI' in R: |
| install.packages('Path2PPI', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- human.ai.irefindex - Data set to predict autophagy induction in _Podospora anserina_
- human.ai.proteins - Data set to predict autophagy induction in _Podospora anserina_
- pa2human.ai.homologs - Data set to predict autophagy induction in _Podospora anserina_
- pa2yeast.ai.homologs - Data set to predict autophagy induction in _Podospora anserina_
- yeast.ai.irefindex - Data set to predict autophagy induction in _Podospora anserina_
- yeast.ai.proteins - Data set to predict autophagy induction in _Podospora anserina_
On BioConductor:Path2PPI-1.37.0(bioc 3.21)Path2PPI-1.36.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
networkinferencesystemsbiologynetworkproteomicspathways
Last updated 2 months agofrom:59d226ca46. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:addReferencegetHybridNetworkgetPPIhomologyScorePath2PPIplot.Path2PPIpredictPPIremoveReferenceshowInteractionshowReferences
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add reference species | addReference |
| Data set to predict autophagy induction in _Podospora anserina_ | ai human.ai.irefindex human.ai.proteins pa2human.ai.homologs pa2yeast.ai.homologs yeast.ai.irefindex yeast.ai.proteins |
| Get hybrid network of the predicted PPI | getHybridNetwork |
| Get predicted PPI | getPPI |
| Computes homology scores | homologyScore |
| Class '"Path2PPI"' | addReference,Path2PPI-method getHybridNetwork,Path2PPI-method getPPI,Path2PPI-method initialize,Path2PPI-method Path2PPI Path2PPI-class plot.Path2PPI,Path2PPI-method predictPPI,Path2PPI-method removeReference,Path2PPI-method show,Path2PPI-method showInteraction,Path2PPI-method showReferences,Path2PPI-method |
| Plots the predicted PPI | plot.Path2PPI |
| Prediction of the PPI | predictPPI |
| Remove reference species | removeReference |
| Information about an interaction | showInteraction showInteraction-methods |
| Information about reference species | showReferences |