Package: STRINGdb 2.25.0
Damian Szklarczyk
STRINGdb: STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
The STRINGdb package provides an R interface to STRING, a protein-protein interaction database and functional enrichment analysis tool (https://string-db.org).
Authors:
STRINGdb_2.25.0.tar.gz
STRINGdb_2.25.0.zip(r-4.7)STRINGdb_2.25.0.zip(r-4.6)STRINGdb_2.25.0.zip(r-4.5)
STRINGdb_2.25.0.tgz(r-4.6-any)STRINGdb_2.25.0.tgz(r-4.5-any)
STRINGdb_2.25.0.tar.gz(r-4.7-any)STRINGdb_2.25.0.tar.gz(r-4.6-any)
STRINGdb_2.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
STRINGdb/json (API)
| # Install 'STRINGdb' in R: |
| install.packages('STRINGdb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- diff_exp_example1 - Example of microarray data
- interactions_example - Example of a protein-protein interactions sorted data frame
On BioConductor:STRINGdb-2.25.0(bioc 3.24)STRINGdb-2.24.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:7733ddc025. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 139 | ||
| linux-devel-x86_64 | OK | 335 | ||
| source / vignettes | OK | 288 | ||
| linux-release-x86_64 | OK | 289 | ||
| macos-release-arm64 | OK | 229 | ||
| macos-oldrel-arm64 | OK | 236 | ||
| windows-devel | OK | 235 | ||
| windows-release | OK | 224 | ||
| windows-oldrel | OK | 218 | ||
| wasm-release | OK | 157 |
Exports:delColDfdownloadAbsentFiledownloadAbsentFileSTRINGmulti_map_dfrenameColDfSTRINGdb
Dependencies:askpassbitbit64bitopsblobcachemcaToolschronclicpp11curlDBIfastmapgluegplotsgsubfngtoolshashhttrigraphjsonliteKernSmoothlatticelifecyclemagrittrMatrixmemoisemimeopensslpkgconfigplotrixplyrpngprotoR6RColorBrewerRcpprlangRSQLitesqldfsysvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add_diff_exp_color | \S4method{add_diff_exp_color}{STRINGdb} |
| add_proteins_description | \S4method{add_proteins_description}{STRINGdb} |
| coeffOfvar | coeffOfvar |
| delColDf | delColDf |
| example of microarray data (data processed from GEO GSE9008) | diff_exp_example1 |
| downloadAbsentFile | downloadAbsentFile |
| downloadAbsentFileSTRING | downloadAbsentFileSTRING |
| get_aliases | \S4method{get_aliases}{STRINGdb} |
| get_annotations | \S4method{get_annotations}{STRINGdb} |
| get_annotations_desc | \S4method{get_annotations_desc}{STRINGdb} |
| get_bioc_graph | \S4method{get_bioc_graph}{STRINGdb} |
| get_clusters | \S4method{get_clusters}{STRINGdb} |
| get_enrichment | \S4method{get_enrichment}{STRINGdb} |
| get_graph | \S4method{get_graph}{STRINGdb} |
| get_homologs_besthits | \S4method{get_homologs_besthits}{STRINGdb} |
| get_interaction_partners | \S4method{get_interaction_partners}{STRINGdb} |
| get_interactions | \S4method{get_interactions}{STRINGdb} |
| get_link | \S4method{get_link}{STRINGdb} |
| get_neighbors | \S4method{get_neighbors}{STRINGdb} |
| get_paralogs | \S4method{get_paralogs}{STRINGdb} |
| get_png | \S4method{get_png}{STRINGdb} |
| get_ppi_enrichment | \S4method{get_ppi_enrichment}{STRINGdb} |
| get_proteins | \S4method{get_proteins}{STRINGdb} |
| get_subnetwork | \S4method{get_subnetwork}{STRINGdb} |
| get_summary | \S4method{get_summary}{STRINGdb} |
| get_term_proteins | \S4method{get_term_proteins}{STRINGdb} |
| example of a protein-protein interactions sorted data frame | interactions_example |
| load | \S4method{load}{STRINGdb} |
| load_all | \S4method{load_all}{STRINGdb} |
| map | \S4method{map}{STRINGdb} |
| mp | \S4method{mp}{STRINGdb} |
| multi_map_df | multi_map_df |
| plot_network | \S4method{plot_network}{STRINGdb} |
| post_payload | \S4method{post_payload}{STRINGdb} |
| remove_homologous_interactions | \S4method{remove_homologous_interactions}{STRINGdb} |
| renameColDf | renameColDf |
| set_background | \S4method{set_background}{STRINGdb} |
| Class '"STRINGdb"' | STRINGdb STRINGdb-class |
