Package: wppi 1.15.0
Ana Galhoz
wppi: Weighting protein-protein interactions
Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.
Authors:
wppi_1.15.0.tar.gz
wppi_1.15.0.zip(r-4.5)wppi_1.15.0.zip(r-4.4)wppi_1.15.0.zip(r-4.3)
wppi_1.15.0.tgz(r-4.4-any)wppi_1.15.0.tgz(r-4.3-any)
wppi_1.15.0.tar.gz(r-4.5-noble)wppi_1.15.0.tar.gz(r-4.4-noble)
wppi_1.15.0.tgz(r-4.4-emscripten)wppi_1.15.0.tgz(r-4.3-emscripten)
wppi.pdf |wppi.html✨
wppi/json (API)
NEWS
| # Install 'wppi' in R: |
| install.packages('wppi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/anagalhoz37/wppi/issues
On BioConductor:wppi-1.15.0(bioc 3.21)wppi-1.14.0(bioc 3.20)
graphandnetworknetworkpathwayssoftwaregenesignalinggenetargetsystemsbiologytranscriptomicsannotationgene-ontologygene-prioritizationhuman-phenotype-ontologyomnipathppi-networksrandom-walk-with-restart
Last updated 2 months agofrom:321e17d1d0. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:common_neighborscount_genesfilter_annot_with_networkfunctional_annotgraph_from_opin_omnipathprioritization_genesprocess_annotrandom_walkscore_candidate_genes_from_PPIsubgraph_opweighted_adjwppi_datawppi_go_datawppi_hpo_datawppi_omnipath_data
Dependencies:askpassbackportsbase64encbitbit64bitopsblobbslibcachemcellrangercheckmateclicliprcpp11crayoncurlDBIdigestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhmshtmltoolshttrigraphjquerylibjsonliteknitrlaterlatticelifecycleloggerlubridatemagrittrMatrixmemoisemimeOmnipathRopensslpillarpkgconfigplogrprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRcppRCurlreadrreadxlrematchrlangrmarkdownRSQLitervestsassselectrstringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsvroomwithrxfunXMLxml2yamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Shared neighbors of connected vertices | common_neighbors |
| Number of total genes in an ontology database | count_genes |
| Filter ontology datasets using PPI network object | filter_annot_with_network |
| Functional similarity score based on ontology | functional_annot |
| Igraph object from OmniPath network | graph_from_op |
| Check which genes of interest are or not in OmniPath | in_omnipath |
| Candidate genes prioritization | prioritization_genes |
| Processing of ontology annotations | process_annot |
| Random Walk with Restart (RWR) | random_walk |
| The full WPPI workflow | score_candidate_genes_from_PPI |
| Extract PPI subgraph by genes of interest | subgraph_op |
| Weighted adjacency matrix | weighted_adj |
| The wppi package | wppi |
| Database knowledge for wppi | wppi_data |
| Retrieves data from Gene Ontology (GO) | wppi_go_data |
| Retrieves data from Human Phenotype Ontology (HPO) | wppi_hpo_data |
| Protein-protein interaction data from OmniPath | wppi_omnipath_data |
