{ "_id": "6a114913acfb0bcc41ce82be", "Package": "geneHummus", "Title": "A Pipeline to Define Gene Families in Legumes and Beyond", "Version": "1.0.11", "Authors@R": "c(\nperson(\"Jose V.\", \"Die\", email = \"jose.die@uco.es\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-7506-8590\")),\nperson(\"Moamen M.\", \"Elmassry\", email = \"moamen.elmassry@ttu.edu\", role = c(\"ctb\")),\nperson(\"Kimberly H.\", \"LeBlanc\", email = \"kimberly.leblanc@nih.gov\", role = c(\"ctb\")),\nperson(\"Olaitan I.\", \"Awe\", email = \"laitanawe@gmail.com\", role = c(\"ctb\")),\nperson(\"Allissa\",\"Dillman\", email = \"Allissa.Dillman@nih.gov\", role = c(\"ctb\")),\nperson(\"Ben\", \"Busby\", email = \"Ben.Busby@nih.gov\", role = c(\"aut\")))", "Description": "A pipeline with high specificity and sensitivity in\nextracting proteins from the RefSeq database (National Center\nfor Biotechnology Information). Manual identification of gene\nfamilies is highly time-consuming and laborious, requiring an\niterative process of manual and computational analysis to\nidentify members of a given family. The pipelines implements an\nautomatic approach for the identification of gene families\nbased on the conserved domains that specifically define that\nfamily. See Die et al. (2018) for more\ninformation and examples.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "URL": "https://github.com/NCBI-Hackathons/GeneHummus", "BugReports": "https://github.com/NCBI-Hackathons/GeneHummus/issues", "RoxygenNote": "6.1.1", "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev", "Repository": "https://ncbi-hackathons.r-universe.dev", "Date/Publication": "2020-09-02 21:10:25 UTC", "RemoteUrl": "https://github.com/ncbi-hackathons/genehummus", "RemoteRef": "HEAD", "RemoteSha": "1fb36181760e0c1b91e65dd3cbd05af27010d8c4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 06:25:46 UTC", "User": "root" }, "Author": "Jose V. Die [aut, cre] (ORCID: ),\nMoamen M. Elmassry [ctb],\nKimberly H. LeBlanc [ctb],\nOlaitan I. Awe [ctb],\nAllissa Dillman [ctb],\nBen Busby [aut]", "Maintainer": "Jose V. Die ", "MD5sum": "cb834c673f09e3dfd458f233998108c5", "_user": "ncbi-hackathons", "_type": "src", "_file": "geneHummus_1.0.11.tar.gz", "_fileid": "0d9f42bb9b68a554292f5423e829fa9a5b6ecebcad95e825e3e077cfdbd660eb", "_filesize": 184136, "_sha256": "0d9f42bb9b68a554292f5423e829fa9a5b6ecebcad95e825e3e077cfdbd660eb", "_created": "2026-05-23T06:25:46.000Z", "_published": "2026-05-23T06:28:35.195Z", "_distro": "noble", "_jobs": [ { "job": 77503060133, "time": 136, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7174926498" }, { "job": 77503060134, "time": 130, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7174925983" }, { "job": 77503060124, "time": 138, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7174924231" }, { "job": 77503060127, "time": 120, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7174923229" }, { "job": 77502879995, "time": 205, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7174912607" }, { "job": 77503060115, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7174924575" }, { "job": 77503060154, "time": 89, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7174921785" }, { "job": 77503060152, "time": 90, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7174922116" }, { "job": 77503060160, "time": 88, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7174922231" } ], "_buildurl": "https://github.com/r-universe/ncbi-hackathons/actions/runs/26325661085", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ncbi-hackathons/genehummus", "_commit": { "id": "1fb36181760e0c1b91e65dd3cbd05af27010d8c4", "author": "Jose V. Die ", "committer": "GitHub ", "message": "update for filter with length=1 or >1\n\nif length filter > 1, f. ex. `my_filter <- c(\"B3_DNA\", \"Auxin_resp\")` all the elements have to be found in the sparcle label.", "time": 1599081025 }, "_maintainer": { "name": "Jose V. Die", "email": "jose.die@uco.es", "login": "jdieramon", "twitter": "@jdieramon", "description": "", "uuid": 7064755, "orcid": "0000-0002-7506-8590" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "rentrez", "version": ">= 1.2.1", "role": "Imports" }, { "package": "stringr", "version": ">= 1.4.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 0.8.0.1", "role": "Imports" }, { "package": "httr", "version": ">= 1.4.0", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "curl", "version": ">= 3.3", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "ncbi-hackathons", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 8, "_contributors": [ { "user": "jdieramon", "count": 173, "uuid": 7064755 }, { "user": "dcgenomics", "count": 4, "uuid": 5738421 }, { "user": "moamenelmassry", "count": 4, 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"getArch_labels", "title": "Get the description label for a protein architecture identifier", "topics": [ "getArch_labels" ] }, { "page": "getProteins_from_tax_ids", "title": "Get the RefSeq protein identifiers for the given taxonomic species", "topics": [ "getProteins_from_tax_ids" ] }, { "page": "getProtlinks", "title": "Get the protein identifiers for a given architecture", "topics": [ "getProtlinks" ] }, { "page": "getSparcleArchs", "title": "Get the electronic architecture for a conserved domain", "topics": [ "getSparcleArchs" ] }, { "page": "labels_warning", "title": "Get description label for a protein architecture identifier", "topics": [ "labels_warning" ] }, { "page": "legumesIds", "title": "NCBI taxonomy ids for the legume family", "topics": [ "legumesIds" ] }, { "page": "my_legumes", "title": "ARF proteins per legume specie", "topics": [ "my_legumes" ] }, { "page": "proteins_warning", "title": "Get RefSeq protein identifiers for the given taxonomic species", "topics": [ 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