{ "_id": "69fc548515e4104bb12e1d91", "Package": "webseq", "Type": "Package", "Title": "Access data from biological sequence databases like NCBI, ENA,\nMGnify", "Description": "This package interacts with online biological sequence\ndatabases. It provides functions to search for sequences,\nconvert identifiers and download sequences and associated\nmetadata.", "Version": "0.1", "Date": "2022-01-05", "Author": "Tamas Stirling", "Maintainer": "Tamas Stirling ", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev", "Repository": "https://r-multiverse.r-universe.dev", "Date/Publication": "2024-01-17 08:49:50 UTC", "RemoteUrl": "https://github.com/stitam/webseq", "RemoteRef": "v0.1.0", "RemoteSha": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 08:49:38 UTC", "User": "root" }, "MD5sum": "654e459fe7495b56e450a93e015a02f4", "_user": "r-multiverse", "_type": "src", "_file": "webseq_0.1.tar.gz", "_fileid": "baf06cae1c3364551feb23e8e571734ba94ec53ddd44cbca675404b3a364b774", "_filesize": 162471, "_sha256": "baf06cae1c3364551feb23e8e571734ba94ec53ddd44cbca675404b3a364b774", "_created": "2026-05-07T08:49:38.000Z", "_published": "2026-05-07T08:59:49.622Z", "_distro": "noble", "_jobs": [ { "job": 74780961837, "time": 189, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "6850836848" }, { "job": 74780961818, "time": 197, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6850837532" }, { "job": 74780961836, "time": 185, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "6850960599" }, { "job": 74780961867, "time": 177, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6850955318" }, { "job": 74780348802, "time": 228, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6850768815" }, { "job": 74780961835, "time": 97, "config": "wasm-release", "r": "4.5.1", "check": "OK", "artifact": "6850803548" }, { "job": 74780961829, "time": 156, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "6850823914" }, { "job": 74780961848, "time": 205, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "6850839855" }, { "job": 74780961854, "time": 140, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "6850818311" } ], "_buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/stitam/webseq", "_commit": { "id": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "author": "Tamás Stirling <49147718+stitam@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #51 from stitam/webhis2\n\nDo not use web histories by default with ncbi_link_uid()", "time": 1705481390 }, "_maintainer": { "name": "Tamas Stirling", "email": "stirling.tamas@gmail.com", "login": "stitam", "orcid": "0000-0002-8964-6443", "uuid": 49147718 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "curl", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "rentrez", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "XML", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "stitam", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "stitam", "count": 256, "uuid": 49147718 } ], "_userbio": { "uuid": 161461790, "type": "organization", "name": "R-multiverse", "description": "A community-curated collection of R package releases, powered by R-universe" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/webseq" }, "_devurl": "https://github.com/stitam/webseq", "_searchresults": 1, "_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/webseq.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "ena_query", "extract_accn", "flag_files", "mgnify_endpoints", "mgnify_instance", "mgnify_list", "ncbi_download_genome", "ncbi_get_meta", "ncbi_link_uid", "ncbi_parse", "ncbi_parse_assembly_xml", "ncbi_parse_biosample_txt", "parse_gb_header", "parse_report" ], "_datasets": [ { "name": "examples", "title": "Examples", "object": "examples", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "ena_query", "title": "Retrieve sequences from ENA", "topics": [ "ena_query" ] }, { "page": "examples", "title": "Examples", "topics": [ "examples" ] }, { "page": "extract_accn", "title": "Extract Accession Numbers from a parsed assembly report", "topics": [ "extract_accn" ] }, { "page": "flag_files", "title": "Flag files to keep for analysis", "topics": [ "flag_files" ] }, { "page": "mgnify_endpoints", "title": "MGnify endpoints", "topics": [ "mgnify_endpoints" ] }, { "page": "mgnify_instance", "title": "Search for a specific entry in MGnify", "topics": [ "mgnify_instance" ] }, { "page": "mgnify_list", "title": "Retrieve a list of instances from MGnify", "topics": [ "mgnify_list" ] }, { "page": "ncbi_download_genome", "title": "Download Genomes from NCBI", "topics": [ "ncbi_download_genome" ] }, { "page": "ncbi_get_meta", "title": "Get sequence metadata from NCBI", "topics": [ "ncbi_get_meta" ] }, { "page": "ncbi_get_uid", "title": "Get UID-s from NCBI databases", "topics": [ "ncbi_get_uid" ] }, { "page": "ncbi_link_uid", "title": "Link UID-s from one NCBI database to another", "topics": [ "ncbi_link_uid" ] }, { "page": "ncbi_meta_assembly", "title": "Retrieve NCBI Assembly metadata", "topics": [ "ncbi_meta_assembly" ] }, { "page": "ncbi_parse", "title": "Parse NCBI sequence metadata", "topics": [ "ncbi_parse" ] }, { "page": "ncbi_parse_assembly_xml", "title": "Parse NCBI assembly metadata", "topics": [ "ncbi_parse_assembly_xml" ] }, { "page": "ncbi_parse_biosample_txt", "title": "Parse NCBI BioSample metadata", "topics": [ "ncbi_parse_biosample_txt" ] }, { "page": "ncbi_parse_biosample_xml", "title": "Parse NCBI BioSample metadata", "topics": [ "ncbi_parse_biosample_xml" ] }, { "page": "parse_gb_header", "title": "Parse headers from GenBank files", "topics": [ "parse_gb_header" ] }, { "page": "parse_report", "title": "Parse assembly reports", "topics": [ "parse_report" ] } ], "_readme": "https://github.com/stitam/webseq/raw/v0.1.0/README.md", "_rundeps": [ "askpass", "cli", "cpp11", "curl", "dplyr", "generics", "glue", "httr", "jsonlite", "lifecycle", "magrittr", "mime", "openssl", "pillar", "pkgconfig", "plyr", "purrr", "R6", "Rcpp", "rentrez", "rlang", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XML", "xml2" ], "_vignettes": [ { "source": "ncbi.Rmd", "filename": "ncbi.html", "title": "NCBI", "engine": "knitr::rmarkdown", "headings": [ "Download genome assemblies", "Download metadata", "Parse metadata files" ], "created": "2023-08-23 18:06:14", "modified": "2023-12-10 12:18:12", "commits": 4 } ], "_score": 3.1760912590556813, "_indexed": false, "_nocasepkg": "webseq", "_universes": [ "r-multiverse" ], "_indexurl": "https://stitam.r-universe.dev/webseq", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1", "date": "2026-05-07T08:51:58.000Z", "distro": "noble", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "b35bd788f201e922648097d45e26c03ebdad97b3b42a3e04517a0949b2e19774", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" }, { "r": "4.6.0", "os": "linux", "version": "0.1", "date": "2026-05-07T08:51:57.000Z", "distro": "noble", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "f73754f1b6ee4f22138e787aea8aa2df60123e98d4e5f6090122050097c0fd7f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" }, { "r": "4.5.3", "os": "mac", "version": "0.1", "date": "2026-05-07T08:57:53.000Z", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "1d0c11a9e6f4edcab76a96f9da94355195e545861d0fdc545dbc554ed45d747f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" }, { "r": "4.6.0", "os": "mac", "version": "0.1", "date": "2026-05-07T08:57:40.000Z", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "60107c26ffb6520f66e0c4376f87a70878f14d1fb28fe1694056bc1c20d46696", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" }, { "r": "4.5.1", "os": "wasm", "version": "0.1", "date": "2026-05-07T08:51:35.000Z", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "0dd01cefaee87a424265d63f0466b8beaad5d966167e6760b7c9f9458f61e825", "status": "success", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" }, { "r": "4.7.0", "os": "win", "version": "0.1", "date": "2026-05-07T08:51:12.000Z", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "aecf5e73a2c9cd1c67af60ac1bddb1af745e5351be399694e89a51e80673c47e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" }, { "r": "4.5.3", "os": "win", "version": "0.1", "date": "2026-05-07T08:51:54.000Z", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "bbd052644ca805aa975e49fbde34cca01fcdda0445b0ab8a97e9070c7cddc24d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" }, { "r": "4.6.0", "os": "win", "version": "0.1", "date": "2026-05-07T08:50:53.000Z", "commit": "b710f93da5b8dd8a30fa170cdf3da8da943fbae1", "fileid": "a533d6d68da263008df372e1703a63726e7f596c06f12efdb715154e3e9b959a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/r-multiverse/actions/runs/25485613072" } ] }