Introduction | Preparation of the data | Proteins and interactions of pathways of interest | Get homology files using NCBI BLAST+ | Predict PPI in target species | The Path2PPI object | Add reference species | Predict PPI | Results of the prediction | Plotting the results | Get detailed information about each interaction | Export results | References | Session info | Appendix | Biological evidence of the predicted PPI network | The prediction algorithm | Computing preliminary reference species-specific PPIs | Combining PPIs deduced from each reference species
Package: Path2PPI 1.43.0
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_1.43.0.tar.gz
Path2PPI_1.43.0.zip(r-4.7)Path2PPI_1.43.0.zip(r-4.6)Path2PPI_1.43.0.zip(r-4.5)
Path2PPI_1.43.0.tgz(r-4.6-any)Path2PPI_1.43.0.tgz(r-4.5-any)
Path2PPI_1.43.0.tar.gz(r-4.7-any)Path2PPI_1.43.0.tar.gz(r-4.6-any)
Path2PPI_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Path2PPI/json (API)
| # Install 'Path2PPI' in R: |
| install.packages('Path2PPI', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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-1.43.0(bioc 3.24)Path2PPI-1.42.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
networkinferencesystemsbiologynetworkproteomicspathways
Last updated from:f7b6178e67. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 163 | ||
| linux-devel-x86_64 | NOTE | 173 | ||
| source / vignettes | OK | 189 | ||
| linux-release-x86_64 | NOTE | 227 | ||
| macos-release-arm64 | NOTE | 113 | ||
| macos-oldrel-arm64 | NOTE | 95 | ||
| windows-devel | NOTE | 92 | ||
| windows-release | NOTE | 95 | ||
| windows-oldrel | NOTE | 81 | ||
| wasm-release | OK | 105 |
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 |