{ "_id": "6a0f62bdacfb0bcc41c5c4d4", "Package": "SRAdb", "Type": "Package", "Title": "A compilation of metadata from NCBI SRA and tools", "Version": "1.75.0", "Date": "2024-12-03", "Author": "Jack Zhu and Sean Davis", "Maintainer": "Jack Zhu ", "Description": "The Sequence Read Archive (SRA) is the largest public\nrepository of sequencing data from the next generation of\nsequencing platforms including Roche 454 GS System, Illumina\nGenome Analyzer, Applied Biosystems SOLiD System, Helicos\nHeliscope, and others. However, finding data of interest can be\nchallenging using current tools. SRAdb is an attempt to make\naccess to the metadata associated with submission, study,\nsample, experiment and run much more feasible. This is\naccomplished by parsing all the NCBI SRA metadata into a SQLite\ndatabase that can be stored and queried locally. Fulltext\nsearch in the package make querying metadata very flexible and\npowerful. fastq and sra files can be downloaded for doing\nalignment locally. Beside ftp protocol, the SRAdb has funcitons\nsupporting fastp protocol (ascp from Aspera Connect) for faster\ndownloading large data files over long distance. The SQLite\ndatabase is updated regularly as new data is added to SRA and\ncan be downloaded at will for the most up-to-date metadata.", "License": "Artistic-2.0", "LazyLoad": "yes", "BugReports": "https://github.com/zhujack/SRAdb/issues/new", "biocViews": "Infrastructure, Sequencing, DataImport", "Config/pak/sysreqs": "make", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:34:35 UTC", "RemoteUrl": "https://github.com/bioc/SRAdb", "RemoteRef": "HEAD", "RemoteSha": "0e26d7df6bac72e412ab034af14d364a1189c127", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-21 10:41:09 UTC", "User": "root" }, "MD5sum": "d22aab1a1f23ee447649ad331a9ba4c7", "_user": "bioc", "_type": "src", "_file": "SRAdb_1.75.0.tar.gz", "_fileid": "02fb4ed216e8638333fb3459fbae170c08c72ea53672b3a50f352a5d7aa88ce6", "_filesize": 958549, "_sha256": "02fb4ed216e8638333fb3459fbae170c08c72ea53672b3a50f352a5d7aa88ce6", "_created": "2026-05-21T10:41:09.000Z", "_published": "2026-05-21T19:53:33.710Z", "_jobs": [ { "job": 77256368739, "time": 128, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7133634502" }, { "job": 77256368772, "time": 204, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7133659628" }, { "job": 77256368615, "time": 144, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7133639416" }, { "job": 77256368572, "time": 99, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7133688782" }, { "job": 77256368626, "time": 100, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7133655370" }, { "job": 77256368086, "time": 171, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7133591752" }, { "job": 77256367902, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7145754082" }, { "job": 77256368752, "time": 79, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7133618039" }, { "job": 77256368643, "time": 77, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7133617514" }, { "job": 77256368651, "time": 88, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7133621101" } ], "_bioccheck": { "error": 3, "warning": 4, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26220886594", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SRAdb", "_commit": { "id": "0e26d7df6bac72e412ab034af14d364a1189c127", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379675 }, "_maintainer": { "name": "Jack Zhu", "email": "zhujack@mail.nih.gov", "login": "zhujack8", "description": "", "uuid": 129963942 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "RSQLite", "role": "Depends" }, { "package": "graph", "role": "Depends" }, { "package": "RCurl", "role": "Depends" }, { "package": "R.utils", "role": "Imports" }, { "package": "Rgraphviz", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.75.0", "bioc": "3.24" }, { "branch": "release", "version": "1.74.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "sequencing", "dataimport" ], "_stars": 3, "_contributors": [ { "user": "zhujack8", "count": 81, "uuid": 129963942 }, { "user": "dtenenba", "count": 23, "uuid": 2286826 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "seandavi", "count": 13, "uuid": 92435 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "zhujack", "count": 5, "uuid": 2729794 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 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"startIGV" ], "_help": [ { "page": "SRAdb-package", "title": "Query NCBI SRA metadata within R or from a local SQLite database", "topics": [ "SRAdb-package", "SRAdb" ] }, { "page": "ascpR", "title": "Fasp file downloading using the ascp command line program", "topics": [ "ascpR" ] }, { "page": "ascpSRA", "title": "Fasp SRA data file downloading using the ascp command line program", "topics": [ "ascpSRA" ] }, { "page": "colDescriptions", "title": "Get column descriptions of SRAmetadb.sqlite", "topics": [ "colDescriptions" ] }, { "page": "entityGraph", "title": "Create a new graphNEL object from an input entity matrix or data.frame", "topics": [ "entityGraph" ] }, { "page": "getFASTQfile", "title": "Download SRA fastq files from EBI ENA through ftp or fasp", "topics": [ "getFASTQfile" ] }, { "page": "getFASTQinfo", "title": "Get SRA fastq file information and associated meta data from EBI ENA", "topics": [ "getFASTQinfo" ] }, { "page": "getSRA", "title": "Fulltext search SRA meta data using SQLite fts3 module", "topics": [ "getSRA" ] }, { "page": "getSRAdbFile", "title": "Download and unzip last version of SRAmetadb.sqlite.gz from the server", "topics": [ "getSRAdbFile" ] }, { "page": "getSRAfile", "title": "Download SRA data file through ftp or fasp", "topics": [ "getSRAfile" ] }, { "page": "getSRAinfo", "title": "Get SRA data file information from NCBI SRA", "topics": [ "getSRAinfo" ] }, { "page": "IGVclear", "title": "Clear IGV tracks loaded.", "topics": [ "IGVclear" ] }, { "page": "IGVcollapse", "title": "Collapse tracks in the IGV", "topics": [ "IGVcollapse" ] }, { "page": "IGVgenome", "title": "Set the IGV genome.", "topics": [ "IGVgenome" ] }, { "page": "IGVgoto", "title": "Go to a specified region in IGV.", "topics": [ "IGVgoto" ] }, { "page": "IGVload", "title": "Load data into IGV via remote port call.", "topics": [ "IGVload" ] }, { "page": "IGVsession", "title": "Create an IGV session file", "topics": [ "IGVsession" ] }, { "page": "IGVsnapshot", "title": "Make a file snapshot of the current IGV screen.", "topics": [ "IGVsnapshot" ] }, { "page": "IGVsocket", "title": "Create a Socket Connection to IGV.", "topics": [ "IGVsocket" ] }, { "page": "IGVsort", "title": "Sort an alignment track by the specified option.", "topics": [ "IGVsort" ] }, { "page": "listSRAfile", "title": "List sra, sra-lite or fastq data file names associated with input SRA accessions", "topics": [ "listSRAfile" ] }, { "page": "sraConvert", "title": "Cross-reference between GEO data types", "topics": [ "sraConvert" ] }, { "page": "sraGraph", "title": "Create a new graphNEL object of SRA accessios from SRA full text search", "topics": [ "sraGraph" ] }, { "page": "startIGV", "title": "Start IGV from R with different amount maximum memory support", "topics": [ "startIGV" ] } ], "_readme": "https://github.com/bioc/SRAdb/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "bit", "bit64", "bitops", "blob", "cachem", "cli", "cpp11", "DBI", "fastmap", "generics", "glue", "graph", "lifecycle", "memoise", "pkgconfig", "R.methodsS3", "R.oo", "R.utils", "RCurl", "rlang", "RSQLite", "vctrs" ], "_vignettes": [ { "source": "SRAdb.Rnw", "filename": "SRAdb.pdf", "title": "Using SRAdb to Query the Sequence Read Archive", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:12:58", "modified": "2019-12-24 10:40:40", "commits": 7 } ], "_score": 7.732393759822968, "_indexed": true, "_nocasepkg": "sradb", "_universes": [ "bioc", "zhujack8", "zhujack" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.75.0", "date": "2026-05-21T10:44:30.000Z", "distro": "noble", "commit": "0e26d7df6bac72e412ab034af14d364a1189c127", "fileid": "47aea4bbd3c2c82d5030a3d446240ae227a0a0c141c832a0757115fb5e040415", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26220886594" }, { "r": "4.6.0", "os": "linux", "version": "1.75.0", "date": "2026-05-21T10:43:31.000Z", "distro": "noble", "commit": 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