{ "_id": "6a173438acfb0bcc41d941fa", "Package": "rtemis.a3", "Title": "Amino Acid Annotation (A3) Format", "Version": "0.5.3", "Date": "2026-04-24", "Authors@R": "person(given = \"E.D.\", family = \"Gennatas\", role = c(\"aut\", \"cre\", \"cph\"),\nemail = \"gennatas@gmail.com\",\ncomment = c(ORCID = \"0000-0001-9280-3609\"))", "Description": "Implements the Amino Acid Annotation (A3) format using\n'S7' classes. The A3 format is a structured schema for\nannotating amino acid sequences with site, region,\npost-translational modification (PTM), processing event, and\nvariant information. Provides functions to create, read, and\nwrite A3 objects, and to import annotations from 'UniProt',\n'AlphaFold', 'PDBe', 'ClinVar', and 'Ensembl'.", "URL": "https://a3.rtemis.org", "BugReports": "https://github.com/rtemis-org/a3/issues", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Repository": "https://rtemis-org.r-universe.dev", "Date/Publication": "2026-05-07 18:13:20 UTC", "RemoteUrl": "https://github.com/rtemis-org/a3", "RemoteRef": "HEAD", "RemoteSha": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "RemoteSubdir": "r", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 18:09:38 UTC", "User": "root" }, "Author": "E.D. Gennatas [aut, cre, cph] (ORCID:\n)", "Maintainer": "E.D. Gennatas ", "MD5sum": "7a6f4c552024c326f533edd9898da860", "_user": "rtemis-org", "_type": "src", "_file": "rtemis.a3_0.5.3.tar.gz", "_fileid": "daac079c48d0116dbc79d6ca91bf08d63221d2f2339cff8c898a1ae4c5dfb3a4", "_filesize": 143172, "_sha256": "daac079c48d0116dbc79d6ca91bf08d63221d2f2339cff8c898a1ae4c5dfb3a4", "_created": "2026-05-27T18:09:38.000Z", "_published": "2026-05-27T18:13:12.418Z", "_distro": "noble", "_jobs": [ { "job": 78142705898, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7248189452" }, { "job": 78142705837, "time": 132, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7248185777" }, { "job": 78142705795, "time": 94, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7248172091" }, { "job": 78142705807, "time": 103, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7248174938" }, { "job": 78142180223, "time": 172, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7248136091" }, { "job": 78142705757, "time": 109, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7248177249" }, { "job": 78142705832, "time": 103, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7248175183" }, { "job": 78142705825, "time": 87, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7248169540" }, { "job": 78142705862, "time": 184, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7248204727" } ], "_buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rtemis-org/a3", "_commit": { "id": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "author": "Stathis Gennatas ", "committer": "Stathis Gennatas ", "message": "add installation from registry\n", "time": 1778177600 }, "_maintainer": { "name": "E.D. Gennatas", "email": "gennatas@gmail.com", "login": "egenn", "description": "AI/ML for Precision Medicine & Public Health, Health Data Science; Neuroscience; Visualization; Music", "uuid": 6411723, "orcid": "0000-0001-9280-3609" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "rtemis.core", "role": "Imports" }, { "package": "S7", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "httr", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "seqinr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "rtemis-org", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-12", "n": 2 }, { "week": "2026-13", "n": 78 }, { "week": "2026-14", "n": 34 }, { "week": "2026-15", "n": 13 }, { "week": "2026-16", "n": 17 }, { "week": "2026-17", "n": 17 }, { "week": "2026-18", "n": 6 }, { "week": "2026-19", "n": 4 } ], "_tags": [ { "name": "RtemisA3-v0.1.0", "date": "2026-05-07" } ], "_stars": 2, "_contributors": [ { "user": "egenn", "count": 276, "uuid": 6411723 } ], "_userbio": { "uuid": 162761267, "type": "organization", "name": "rtemis AI/ML", "description": "Machine Learning/Visualization/Agentic AI" }, "_downloads": { "count": 443, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rtemis.a3" }, "_devurl": "https://github.com/rtemis-org/a3", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/rtemis.a3.html", "manual.pdf" ], "_homeurl": "https://github.com/rtemis-org/a3", "_realowner": "rtemis-org", "_cranurl": true, "_releases": [ { "version": "0.5.3", "date": "2026-04-28" } ], "_exports": [ "aa_sub", "annotation_position", "annotation_range", "annotation_variant", "clinvar_variants", "concat", "create_A3", "gene2sequence", "get_alphafold", "pdb_annotations", "read_A3json", "uniprot_sequence", "uniprot_to_A3", "write_A3json" ], "_help": [ { "page": "rtemis.a3-package", "title": "rtemis.a3: Amino Acid Annotation format", "topics": [ "rtemis.a3-package", "rtemis.a3" ] }, { "page": "aa_sub", "title": "Perform amino acid substitutions", "topics": [ "aa_sub" ] }, { "page": "annotation_position", "title": "Create position-based annotations for A3", "topics": [ "annotation_position" ] }, { "page": "annotation_range", "title": "Create range-based annotations for A3", "topics": [ "annotation_range" ] }, { "page": "annotation_variant", "title": "Create variant annotations for A3", "topics": [ "annotation_variant" ] }, { "page": "clinvar_variants", "title": "Fetch ClinVar variants for a gene and parse them into A3Variant objects", "topics": [ "clinvar_variants" ] }, { "page": "concat", "title": "Concatenate character vector to single string for sequence input", "topics": [ "concat" ] }, { "page": "create_A3", "title": "Create an A3 object from sequence, annotations, and metadata", "topics": [ "create_A3" ] }, { "page": "gene2sequence", "title": "Get the coding sequence of a gene", "topics": [ "gene2sequence" ] }, { "page": "get_alphafold", "title": "Get AlphaFold info for a given UniProt ID", "topics": [ "get_alphafold" ] }, { "page": "pdb_annotations", "title": "Fetch PDB structural annotations for a UniProt accession", "topics": [ "pdb_annotations" ] }, { "page": "read_A3json", "title": "Read 'A3' object from JSON file", "topics": [ "read_A3json" ] }, { "page": "uniprot_sequence", "title": "Fetch a protein sequence from UniProt", "topics": [ "uniprot_sequence" ] }, { "page": "uniprot_to_A3", "title": "Fetch a UniProt entry and parse it into an A3 object", "topics": [ "uniprot_to_A3" ] }, { "page": "write_A3json", "title": "Write 'A3' object to JSON file", "topics": [ "write_A3json" ] } ], "_pkglogo": "https://github.com/rtemis-org/a3/raw/HEAD/r/man/figures/logo.svg", "_readme": "https://github.com/rtemis-org/a3/raw/HEAD/r/README.md", "_rundeps": [ "cli", "data.table", "rtemis.core", "S7" ], "_score": 3.9030899869919438, "_indexed": true, "_nocasepkg": "rtemis.a3", "_universes": [ "rtemis-org", "egenn" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.5.3", "date": "2026-05-27T18:11:55.000Z", "distro": "noble", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "97a5fb230b6b52df3a00f2b8c160a541e6e13c0a9983b8b40b66f6702c242fec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" }, { "r": "4.6.0", "os": "linux", "version": "0.5.3", "date": "2026-05-27T18:11:49.000Z", "distro": "noble", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "789e923d8f10e4611a7ed7c63929c9f26971e1138027bc249d0c48267b81212b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" }, { "r": "4.5.3", "os": "mac", "version": "0.5.3", "date": "2026-05-27T18:11:13.000Z", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "85bc322a7c17e2f1d4270793c9fb3ffdfb240c7ae5e4baedeb251bb194361b8a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" }, { "r": "4.6.0", "os": "mac", "version": "0.5.3", "date": "2026-05-27T18:11:20.000Z", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "534cf95c04ba6c3225f8cee8ebd1d4474cffc7f8ecfb08e3b93dbddf495ea2f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" }, { "r": "4.6.0", "os": "wasm", "version": "0.5.3", "date": "2026-05-27T18:11:42.000Z", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "303a20f53596b880cf97bd8d278d560d696bb173d9c61c3b961fa41de385e1cb", "status": "success", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" }, { "r": "4.7.0", "os": "win", "version": "0.5.3", "date": "2026-05-27T18:11:12.000Z", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "581702ec13d88c67d9edaabbd61d27a1ebc11e6ef8ad2a9e179c51496063a24c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" }, { "r": "4.5.3", "os": "win", "version": "0.5.3", "date": "2026-05-27T18:10:58.000Z", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "3d4a8429584d418f9e84824671759522ad5b09fb59b25d217ff8395110f9ac61", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" }, { "r": "4.6.0", "os": "win", "version": "0.5.3", "date": "2026-05-27T18:12:32.000Z", "commit": "c23726c0b8e0abc441c53a00f6575b355648b3b3", "fileid": "878e4de6d5696d1c071cd9760ca092cae30920755b1bb5a6be31082f8f692bf9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rtemis-org/actions/runs/26529517618" } ] }