{ "_id": "6aeb9a152e87f76f20ad2a5e", "Package": "STRINGdb", "Type": "Package", "Title": "STRINGdb - Protein-Protein Interaction Networks and Functional\nEnrichment Analysis", "Version": "2.25.3", "Date": "2026-11-04", "Author": "Andrea Franceschini ", "Maintainer": "Damian Szklarczyk ", "Description": "The STRINGdb package provides an R interface to STRING, a\nprotein-protein interaction database and functional enrichment\nanalysis tool (https://string-db.org).", "License": "GPL-2", "biocViews": "Network", "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-11-04 14:15:04 UTC", "RemoteUrl": "https://github.com/bioc/STRINGdb", "RemoteRef": "HEAD", "RemoteSha": "88df545b77084805644c43a3e42ef29e626dd786", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-04 20:40:41 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "STRINGdb_2.25.3.tar.gz", "_fileid": "https://r2.ropensci.org/edcb8c267f19d799aed5da9d79447d85e5dd2917fb759a865c6d39e1c3a84851", "_filesize": 4348670, "_sha256": "edcb8c267f19d799aed5da9d79447d85e5dd2917fb759a865c6d39e1c3a84851", "_expires": "2027-02-12T20:48:19.000Z", "_created": "2026-11-04T20:40:41.000Z", "_published": "2026-11-04T20:48:21.067Z", "_upstream": "https://github.com/bioc/STRINGdb", "_status": "success", "_maintainer": { "name": "Damian Szklarczyk", "email": "damian.szklarczyk@imls.uzh.ch", "login": "damianimls", "description": "", "uuid": 55656176 }, "_jobs": [ { "job": 126850955055, "time": 122, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13360754086" }, { "job": 126850955369, "time": 363, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13362855113" }, { "job": 126850955203, "time": 412, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13362416490" }, { "job": 126850955165, "time": 216, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13361707562" }, { "job": 126850955040, "time": 340, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13361848368" }, { "job": 126848477005, "time": 270, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13362410517" }, { "job": 126850955376, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13360489662" }, { "job": 126850955118, "time": 202, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13361527891" }, { "job": 126850955124, "time": 244, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13361697661" }, { "job": 126850955277, "time": 228, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13362545546" } ], "_bioccheck": { "error": 2, "warning": 8, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41908169728", "_commit": { "id": "88df545b77084805644c43a3e42ef29e626dd786", "author": "Damian ", "committer": "Damian ", "message": "Fix wrong map() results, get_summary() default and payload images\n\nmap() gave wrong results without a warning in three cases:\n- Missing (NA) or empty identifiers were mapped to a real protein. The\n normalization of the aliases (iconv from Windows-1252) turned aliases\n with bytes that Windows-1252 does not define, such as the hyphen U+2010\n in \"spine-associated RapGAP 3\", into NA, and merge() matched them to\n every NA identifier: for human, every row without a gene name got\n 9606.ENSP00000222345, and removeUnmappedRows = TRUE kept those rows.\n- With several identifier columns, the identifiers were written back by\n position after the rows had been reordered, so they no longer matched\n the rest of their rows.\n- With takeFirst = FALSE, the identifiers came back upper-cased.\n\nNow an NA or empty identifier is never mapped, every row keeps its own\nidentifiers as given, and the rows keep the order of the input. The\nundefined bytes are kept as byte codes, so those aliases can be mapped, and\nget_aliases() contains no NA aliases. The columns, their order and the\norder of the repeated rows of takeFirst = FALSE are unchanged; for the\nvignette's example and the human aliases of STRING 12.5 the output is\nidentical to before.\n\nget_summary() gets the default required_score = NULL (the score_threshold\nof the object), so get_summary(string_ids) works as documented.\npost_payload() sends logo_imgF and legend_imgF with httr's upload_file\ninstead of RCurl's fileUpload, which the package no longer imports. New\noffline unit tests; the help of map, multi_map_df and get_summary describes\nthe behaviour.\n", "time": 1793801704 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.14.0", "role": "Depends" }, { "package": "png", "role": "Imports" }, { "package": "sqldf", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "hash", "role": "Imports" }, { "package": "plotrix", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 10, "_updates": [ { "week": "2026-15", "n": 5 }, { "week": "2026-16", "n": 1 }, { "week": "2026-18", "n": 2 }, { "week": "2026-40", "n": 4 }, { "week": "2026-44", "n": 2 }, { "week": "2026-45", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.25.2", "bioc": "3.24", "repository": "bioc", "r": "4.6.0" }, { "branch": "release", "version": "2.24.2", "bioc": "3.23", "repository": "bioc", "r": "4.6.0" } ], "_topics": [ "network" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 484, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 6232, "source": "https://www.bioconductor.org/packages/stats/bioc/STRINGdb" }, "_mentions": 82, "_searchresults": 861, "_abi": { "exports": [ { "key": "STRINGdb::STRINGdb", "hash": "8e7f6e3962b66c5c" }, { "key": "STRINGdb::igraph", "hash": "c187417c40576831" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/STRINGdb.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "delColDf", "downloadAbsentFile", "downloadAbsentFileSTRING", "multi_map_df", "renameColDf", "STRINGdb" ], "_datasets": [ { "name": "diff_exp_example1", "title": "example of microarray data (data processed from GEO GSE9008)", "object": "diff_exp_example1", "file": "diff_exp_example1.rda", "class": [ "data.frame" ], "fields": [ "pvalue", "logFC", "gene" ], "rows": 20861, "table": true, "tojson": true }, { "name": "interactions_example", "title": "example of a protein-protein interactions sorted data frame", "object": "interactions_example", "file": "interactions_example.rda", "class": [ "data.frame" ], "fields": [ "proteinA", "proteinB", "score" ], "rows": 70000, "table": true, "tojson": true } ], "_help": [ { "page": "add_diff_exp_color", "title": "add_diff_exp_color", "topics": [ "\\S4method{add_diff_exp_color}{STRINGdb}" ] }, { "page": "add_proteins_description", "title": "add_proteins_description", "topics": [ "\\S4method{add_proteins_description}{STRINGdb}" ] }, { "page": "coeffOfvar", "title": "coeffOfvar", "topics": [ "coeffOfvar" ] }, { "page": "delColDf", "title": "delColDf", "topics": [ "delColDf" ] }, { "page": "diff_exp_example1", "title": "example of microarray data (data processed from GEO GSE9008)", "topics": [ "diff_exp_example1" ] }, { "page": "downloadAbsentFile", "title": "downloadAbsentFile", "topics": [ "downloadAbsentFile" ] }, { "page": "downloadAbsentFileSTRING", "title": "downloadAbsentFileSTRING", "topics": [ "downloadAbsentFileSTRING" ] }, { "page": "get_aliases", "title": "get_aliases", "topics": [ "\\S4method{get_aliases}{STRINGdb}" ] }, { "page": "get_annotations", "title": "get_annotations", "topics": [ "\\S4method{get_annotations}{STRINGdb}" ] }, { "page": "get_annotations_desc", "title": "get_annotations_desc", "topics": [ "\\S4method{get_annotations_desc}{STRINGdb}" ] }, { "page": "get_bioc_graph", "title": "get_bioc_graph", "topics": [ "\\S4method{get_bioc_graph}{STRINGdb}" ] }, { "page": "get_clusters", "title": "get_clusters", "topics": [ "\\S4method{get_clusters}{STRINGdb}" ] }, { "page": "get_enrichment", "title": "get_enrichment", "topics": [ "\\S4method{get_enrichment}{STRINGdb}" ] }, { "page": "get_enrichment_figure", "title": "get_enrichment_figure", "topics": [ "\\S4method{get_enrichment_figure}{STRINGdb}" ] }, { "page": "get_geneset_description", "title": "get_geneset_description", "topics": [ "\\S4method{get_geneset_description}{STRINGdb}" ] }, { "page": "get_graph", "title": "get_graph", "topics": [ "\\S4method{get_graph}{STRINGdb}" ] }, { "page": "get_homologs_besthits", "title": "get_homologs_besthits", "topics": [ "\\S4method{get_homologs_besthits}{STRINGdb}" ] }, { "page": "get_interaction_partners", "title": "get_interaction_partners", "topics": [ "\\S4method{get_interaction_partners}{STRINGdb}" ] }, { "page": "get_interactions", "title": "get_interactions", "topics": [ "\\S4method{get_interactions}{STRINGdb}" ] }, { "page": "get_link", "title": "get_link", "topics": [ "\\S4method{get_link}{STRINGdb}" ] }, { "page": "get_neighbors", "title": "get_neighbors", "topics": [ "\\S4method{get_neighbors}{STRINGdb}" ] }, { "page": "get_paralogs", "title": "get_paralogs", "topics": [ "\\S4method{get_paralogs}{STRINGdb}" ] }, { "page": "get_png", "title": "get_png", "topics": [ "\\S4method{get_png}{STRINGdb}" ] }, { "page": "get_ppi_enrichment", "title": "get_ppi_enrichment", "topics": [ "\\S4method{get_ppi_enrichment}{STRINGdb}" ] }, { "page": "get_proteins", "title": "get_proteins", "topics": [ "\\S4method{get_proteins}{STRINGdb}" ] }, { "page": "get_subnetwork", "title": "get_subnetwork", "topics": [ "\\S4method{get_subnetwork}{STRINGdb}" ] }, { "page": "get_summary", "title": "get_summary", "topics": [ "\\S4method{get_summary}{STRINGdb}" ] }, { "page": "get_term_proteins", "title": "get_term_proteins", "topics": [ "\\S4method{get_term_proteins}{STRINGdb}" ] }, { "page": "interactions", "title": "example of a protein-protein interactions sorted data frame", "topics": [ "interactions_example" ] }, { "page": "load", "title": "load", "topics": [ "\\S4method{load}{STRINGdb}" ] }, { "page": "load_all", "title": "load_all", "topics": [ "\\S4method{load_all}{STRINGdb}" ] }, { "page": "map", "title": "map", "topics": [ "\\S4method{map}{STRINGdb}" ] }, { "page": "mp", "title": "mp", "topics": [ "\\S4method{mp}{STRINGdb}" ] }, { "page": "multi_map_df", "title": "multi_map_df", "topics": [ "multi_map_df" ] }, { "page": "plot_network", "title": "plot_network", "topics": [ "\\S4method{plot_network}{STRINGdb}" ] }, { "page": "post_payload", "title": "post_payload", "topics": [ "\\S4method{post_payload}{STRINGdb}" ] }, { "page": "remove_homologous_interactions", "title": "remove_homologous_interactions", "topics": [ "\\S4method{remove_homologous_interactions}{STRINGdb}" ] }, { "page": "renameColDf", "title": "renameColDf", "topics": [ "renameColDf" ] }, { "page": "set_background", "title": "set_background", "topics": [ "\\S4method{set_background}{STRINGdb}" ] }, { "page": "STRINGdb-class", "title": "Class '\"STRINGdb\"'", "topics": [ "STRINGdb", "STRINGdb-class" ] } ], "_rundeps": [ "askpass", "bit", "bit64", "bitops", "blob", "cachem", "caTools", "chron", "cli", "cpp11", "curl", "DBI", "fastmap", "glue", "gplots", "gsubfn", "gtools", "hash", "httr", "igraph", "jsonlite", "KernSmooth", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "openssl", "pkgconfig", "plotrix", "plyr", "png", "proto", "R6", "RColorBrewer", "Rcpp", "rlang", "RSQLite", "sqldf", "sys", "vctrs" ], "_vignettes": [ { "source": "STRINGdb.Rnw", "filename": "STRINGdb.pdf", "title": "STRINGdb Vignette", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:32:25", "modified": "2026-09-29 10:44:06", "commits": 22 } ], "_score": 8.98490310122147, "_indexed": true, "_nocasepkg": "stringdb", "_universes": [ "bioc", "damianimls" ], "_previous": 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