{ "_id": "6a1982c4acfb0bcc41df9d4d", "Package": "regutools", "Title": "regutools: an R package for data extraction from RegulonDB", "Version": "1.25.0", "Date": "2021-11-15", "Authors@R": "c(\nperson (\"Joselyn\", \"Chavez\", email = \"joselynchavezf@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4974-4591\")),\nperson(\"Carmina\", \"Barberena-Jonas\", email = \"car.barjon@gmail.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0001-7413-638X\")),\nperson(c(\"Jesus\", \"E.\"), \"Sotelo-Fonseca\", email = \"jemilianosf@gmail.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0003-1600-2396\")),\nperson(\"Jose\", \"Alquicira-Hernandez\", email = \"joseah@lcg.unam.mx\",\nrole = c(\"ctb\"), comment = c(ORCID = \"0000-0002-9049-7780\")),\nperson(\"Heladia\", \"Salgado\", email = \"heladia@ccg.unam.mx\",\nrole = c(\"ctb\"), comment = c(ORCID = \"0000-0002-3166-5801\")),\nperson(\"Leonardo\", \"Collado-Torres\", role = c(\"aut\"),\nemail = \"lcolladotor@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2140-308X\")),\nperson(\"Alejandro\", \"Reyes\", email = \"alejandro.reyes.ds@gmail.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0001-8717-6612\"))\n)", "Description": "RegulonDB has collected, harmonized and centralized data\nfrom hundreds of experiments for nearly two decades and is\nconsidered a point of reference for transcriptional regulation\nin Escherichia coli K12. Here, we present the regutools R\npackage to facilitate programmatic access to RegulonDB data in\ncomputational biology. regutools provides researchers with the\npossibility of writing reproducible workflows with automated\nqueries to RegulonDB. The regutools package serves as a bridge\nbetween RegulonDB data and the Bioconductor ecosystem by\nreusing the data structures and statistical methods powered by\nother Bioconductor packages. We demonstrate the integration of\nregutools with Bioconductor by analyzing transcription factor\nDNA binding sites and transcriptional regulatory networks from\nRegulonDB. We anticipate that regutools will serve as a useful\nbuilding block in our progress to further our understanding of\ngene regulatory networks.", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "URL": "https://github.com/ComunidadBioInfo/regutools", "BugReports": "https://support.bioconductor.org/t/regutools", "biocViews": "GeneRegulation, GeneExpression, SystemsBiology,\nNetwork,NetworkInference,Visualization, Transcription", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\npython3 xz-utils libzmq3-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:39 UTC", "RemoteUrl": "https://github.com/bioc/regutools", "RemoteRef": "HEAD", "RemoteSha": "7f9073361976c8aed050c7498fee6c84285adfc7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 10:20:08 UTC", "User": "root" }, "Author": "Joselyn Chavez [aut, cre] (ORCID:\n),\nCarmina Barberena-Jonas [aut] (ORCID:\n),\nJesus E. Sotelo-Fonseca [aut] (ORCID:\n),\nJose Alquicira-Hernandez [ctb] (ORCID:\n),\nHeladia Salgado [ctb] (ORCID: ),\nLeonardo Collado-Torres [aut] (ORCID:\n),\nAlejandro Reyes [aut] (ORCID: )", "Maintainer": "Joselyn Chavez ", "MD5sum": "359b3e5ea70e42ca1b853939cd29aa66", "_user": "bioc", "_type": "src", "_file": "regutools_1.25.0.tar.gz", "_fileid": "e33a197c6fe89267520178bfb4abeb5fc9b1c636379b2bede09fb411ee4a0002", "_filesize": 325645, "_sha256": "e33a197c6fe89267520178bfb4abeb5fc9b1c636379b2bede09fb411ee4a0002", "_created": "2026-05-29T10:20:08.000Z", "_published": "2026-05-29T12:12:52.084Z", "_jobs": [ { "job": 78482388650, "time": 206, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7288512215" }, { "job": 78482388682, "time": 608, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7288629581" }, { "job": 78482388722, "time": 573, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7288619874" }, { "job": 78482388699, "time": 327, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7290343212" }, { "job": 78482388686, "time": 351, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7290350991" }, { "job": 78481398755, "time": 415, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288449875" }, { "job": 78482388688, "time": 180, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288504477" }, { "job": 78482388697, "time": 558, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7288615821" }, { "job": 78482388670, "time": 531, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7288608173" }, { "job": 78482388705, "time": 603, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7288628896" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26631536295", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/regutools", "_commit": { "id": "7f9073361976c8aed050c7498fee6c84285adfc7", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380759 }, "_maintainer": { "name": "Joselyn Chavez", "email": "joselynchavezf@gmail.com", "login": "josschavezf", "twitter": "@josschavezf1", "description": "", "uuid": 29151402, "orcid": "0000-0002-4974-4591" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "AnnotationHub", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "Gviz", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "RCy3", "role": "Imports" }, { "package": "RSQLite", "role": 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"networkinference", "visualization", "transcription", "bioconductor", "cdsb", "regulondb" ], "_stars": 5, "_contributors": [ { "user": "josschavezf", "count": 167, "uuid": 29151402 }, { "user": "joseah", "count": 91, "uuid": 7775770 }, { "user": "lcolladotor", "count": 70, "uuid": 2288213 }, { "user": "areyesq89", "count": 26, "uuid": 12632413 }, { "user": "jemilianosf", "count": 18, "uuid": 17206038 }, { "user": "carbarjon", "count": 18, "uuid": 17257470 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 337, "source": "https://www.bioconductor.org/packages/stats/bioc/regutools" }, "_devurl": "https://github.com/comunidadbioinfo/regutools", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/regutools.html", "manual.pdf" ], "_homeurl": "https://github.com/comunidadbioinfo/regutools", "_realowner": "bioc", "_cranurl": false, "_exports": [ "build_condition", "connect_database", "convert_to_biostrings", "convert_to_granges", "existing_intervals", "existing_partial_match", "get_binding_sites", "get_dataset", "get_dna_objects", "get_gene_regulators", "get_gene_synonyms", "get_regulatory_network", "get_regulatory_summary", "guess_id", "list_attributes", "list_datasets", "non_existing_intervals", "plot_dna_objects", "regulondb" ], "_help": [ { "page": "build_condition", "title": "Construct logical condition to query database", "topics": [ "build_condition" ] }, { "page": "connect_database", "title": "Connect to the regulondb database", "topics": [ "connect_database" ] }, { "page": "convert_to_biostrings", "title": "Function to convert output of regulondb queries to Biostrings objects", "topics": [ "convert_to_biostrings" ] }, { "page": "convert_to_granges", "title": "Function to convert output of regulondb queries to GenomicRanges objects", "topics": [ "convert_to_granges" ] }, { "page": "existing_intervals", "title": "Constructs a particular logical condition to query database", "topics": [ "existing_intervals" ] }, { "page": "existing_partial_match", "title": "Constructs a logical condition to query database", "topics": [ "existing_partial_match" ] }, { "page": "get_binding_sites", "title": "Get the binding sites for a Transcription Factor (TF)", "topics": [ "get_binding_sites" ] }, { "page": "get_dataset", "title": "Extract data from RegulonDB", "topics": [ "get_dataset" ] }, { "page": "get_dna_objects", "title": "Retrieve genomic elements from regulonDB", "topics": [ "get_dna_objects" ] }, { "page": "get_gene_regulators", "title": "Get TFs or genes that regulate the genes of interest", "topics": [ "get_gene_regulators" ] }, { "page": "get_gene_synonyms", "title": "Retrieve gene synonyms", "topics": [ "get_gene_synonyms" ] }, { "page": "get_regulatory_network", "title": "Return complete regulatory network.", "topics": [ "get_regulatory_network" ] }, { "page": "get_regulatory_summary", "title": "Return summary of gene regulation.", "topics": [ "get_regulatory_summary" ] }, { "page": "guess_id", "title": "Guess gene id type", "topics": [ "guess_id" ] }, { "page": "list_attributes", "title": "List attributes/fields from a dataset/table", "topics": [ "list_attributes" ] }, { "page": "list_datasets", "title": "List available datasets in RegulonDB database", "topics": [ "list_datasets" ] }, { "page": "non_existing_intervals", "title": "Constructs a logical condition to query database", "topics": [ "non_existing_intervals" ] }, { "page": "plot_dna_objects", "title": "Plot annotation elements within genomic region", "topics": [ "plot_dna_objects" ] }, { "page": "regulondb", "title": "Constructor function of a regulondb class", "topics": [ "build_regulondb", "regulondb" ] }, { "page": "regulondb_result-class", "title": "The regulondb_results class", "topics": [ "regulondb_result-class" ] }, { "page": "regulondb-class", "title": "The regulondb class", "topics": [ "regulondb-class" ] }, { "page": "regulondb-methods", "title": "Methods for regulondb objects", "topics": [ "show", "show,regulondb-method" ] } ], "_pkglogo": "https://github.com/bioc/regutools/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/regutools/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "AnnotationHub", "askpass", "backports", "base64enc", "base64url", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "BiocVersion", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", 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