{ "_id": "6a494d75f6c47c4419499c48", "Package": "GA4GHclient", "Type": "Package", "Title": "A Bioconductor package for accessing GA4GH API data servers", "Version": "1.37.0", "Authors@R": "c(person(\"Welliton\", \"Souza\", email = \"well309@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Benilton\", \"Carvalho\", email = \"benilton@unicamp.br\", role = \"ctb\"),\nperson(\"Cristiane\", \"Rocha\", email = \"crirocha@gmail.com\", role = \"ctb\"))", "Description": "GA4GHclient provides an easy way to access public data\nservers through Global Alliance for Genomics and Health (GA4GH)\ngenomics API. It provides low-level access to GA4GH API and\ntranslates response data into Bioconductor-based class objects.", "License": "GPL (>= 2)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "URL": "https://github.com/labbcb/GA4GHclient", "BugReports": "https://github.com/labbcb/GA4GHclient/issues", "biocViews": "DataRepresentation, ThirdPartyClient", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:21 UTC", "RemoteUrl": "https://github.com/bioc/GA4GHclient", "RemoteRef": "HEAD", "RemoteSha": "7d0549e51e221273d102096a759fb0636296f991", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 21:34:06 UTC", "User": "root" }, "Author": "Welliton Souza [aut, cre],\nBenilton Carvalho [ctb],\nCristiane Rocha [ctb]", "Maintainer": "Welliton Souza ", "_user": "bioc", "_type": "src", "_file": "GA4GHclient_1.37.0.tar.gz", "_fileid": "https://r2.ropensci.org/f14b7bc14b11aa2968e678bfbb8de2eb7a8e1781b18d5582efbac363361a78bc", "_filesize": 491674, "_sha256": "f14b7bc14b11aa2968e678bfbb8de2eb7a8e1781b18d5582efbac363361a78bc", "_expires": "2026-10-12T18:14:11.000Z", "_created": "2026-07-03T21:34:06.000Z", "_published": "2026-07-04T18:14:12.998Z", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088", "_status": "success", "_upstream": "https://github.com/bioc/GA4GHclient", "_commit": { "id": "7d0549e51e221273d102096a759fb0636296f991", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380321 }, "_maintainer": { "name": "Welliton Souza", "email": "well309@gmail.com", "login": "wdesouza", "description": "Data Engineer", "uuid": 645272 }, "_distro": "resolute", "_jobs": [ { "job": 85155344323, "time": 295, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8075120725" }, { "job": 85155344324, "time": 453, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8075148020" }, { "job": 85155344444, "time": 457, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8075148626" }, { "job": 85155344306, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8075105787" }, { "job": 85155344305, "time": 338, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8075127689" }, { "job": 85155344309, "time": 338, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8075067569" }, { "job": 85155344256, "time": 246, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8075112009" }, { "job": 85155344432, "time": 345, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8075129589" }, { "job": 85155344402, "time": 330, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "8075126818" }, { "job": 85155344325, "time": 362, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8075132227" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "S4Vectors", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "VariantAnnotation", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Suggests" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "datarepresentation", "thirdpartyclient" ], "_stars": 1, "_contributors": [ { "user": "wdesouza", "count": 13, "uuid": 645272 }, { "user": "hpages", "count": 2, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/labbcb/ga4ghclient", "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GA4GHclient.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/labbcb/ga4ghclient", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getBiosample", "getCallSet", "getDataset", "getExpressionLevel", "getFeature", "getFeatureSet", "getIndividual", "getReadGroupSet", "getReference", "getReferenceSet", "getRnaQuantification", "getRnaQuantificationSet", "getVariant", "getVariantAnnotationSet", "getVariantSet", "HGVSnames", "listReferenceBases", "makeVCFFromGA4GHResponse", "makeVCFHeaderFromGA4GHResponse", "searchBiosamples", "searchCallSets", "searchDatasets", "searchExpressionLevels", "searchFeatures", "searchFeatureSets", "searchIndividuals", "searchPhenotypeAssociations", "searchPhenotypeAssociationSets", "searchReadGroupSets", "searchReads", "searchReferences", "searchReferenceSets", "searchRnaQuantifications", "searchRnaQuantificationSets", "searchVariantAnnotations", "searchVariantAnnotationSets", "searchVariants", "searchVariantsByGRanges", "searchVariantSets" ], "_help": [ { "page": "GA4GHclient-package", "title": "A Bioconductor package for accessing GA4GH API data server", "topics": [ "GA4GHclient-package", "GA4GHclient" ] }, { "page": "getBiosample", "title": "getBiosample function", "topics": [ "getBiosample" ] }, { "page": "getCallSet", "title": "getCallSet function", "topics": [ "getCallSet" ] }, { "page": "getDataset", "title": "getDataset function", "topics": [ "getDataset" ] }, { "page": "getExpressionLevel", "title": "getExpressionLevel function", "topics": [ "getExpressionLevel" ] }, { "page": "getFeature", "title": "getFeature function", "topics": [ "getFeature" ] }, { "page": "getFeatureSet", "title": "getFeatureSet function", "topics": [ "getFeatureSet" ] }, { "page": "getIndividual", "title": "getIndividual function", "topics": [ "getIndividual" ] }, { "page": "getReadGroupSet", "title": "getReadGroupSet function", "topics": [ "getReadGroupSet" ] }, { "page": "getReference", "title": "getReference function", "topics": [ "getReference" ] }, { "page": "getReferenceSet", "title": "getReferenceSet function", "topics": [ "getReferenceSet" ] }, { "page": "getRnaQuantification", "title": "getRnaQuantification function", "topics": [ "getRnaQuantification" ] }, { "page": "getRnaQuantificationSet", "title": "getRnaQuantificationSet function", "topics": [ "getRnaQuantificationSet" ] }, { "page": "getVariant", "title": "getVariant function", "topics": [ "getVariant" ] }, { "page": "getVariantAnnotationSet", "title": "Gets getVariantAnnotationSet function", "topics": [ "getVariantAnnotationSet" ] }, { "page": "getVariantSet", "title": "getVariantSet function.", "topics": [ "getVariantSet" ] }, { "page": "HGVSnames", "title": "Generate genomic variant data to HGVS nomenclature", "topics": [ "HGVSnames" ] }, { "page": "listReferenceBases", "title": "listReferenceBases function", "topics": [ "listReferenceBases" ] }, { "page": "makeVCFFromGA4GHResponse", "title": "makeVCFFromGA4GHResponse function", "topics": [ "makeVCFFromGA4GHResponse" ] }, { "page": "makeVCFHeaderFromGA4GHResponse", "title": "makeVCFHeaderFromGA4GHResponse function", "topics": [ "makeVCFHeaderFromGA4GHResponse" ] }, { "page": "searchBiosamples", "title": "searchBiosamples function", "topics": [ "searchBiosamples" ] }, { "page": "searchCallSets", "title": "searchCallSets function", "topics": [ "searchCallSets" ] }, { "page": "searchDatasets", "title": "searchDatasets function", "topics": [ "searchDatasets" ] }, { "page": "searchExpressionLevels", "title": "searchExpressionLevels function", "topics": [ "searchExpressionLevels" ] }, { "page": "searchFeatures", "title": "searchFeatures function", "topics": [ "searchFeatures" ] }, { "page": "searchFeatureSets", "title": "searchFeatureSets function", "topics": [ "searchFeatureSets" ] }, { "page": "searchIndividuals", "title": "searchIndividuals function", "topics": [ "searchIndividuals" ] }, { "page": "searchPhenotypeAssociations", "title": "searchPhenotypeAssociations function", "topics": [ "searchPhenotypeAssociations" ] }, { "page": "searchPhenotypeAssociationSets", "title": "searchPhenotypeAssociationSets function", "topics": [ "searchPhenotypeAssociationSets" ] }, { "page": "searchReadGroupSets", "title": "searchReadGroupSets function", "topics": [ "searchReadGroupSets" ] }, { "page": "searchReads", "title": "searchReads function", "topics": [ "searchReads" ] }, { "page": "searchReferences", "title": "searchReferences function", "topics": [ "searchReferences" ] }, { "page": "searchReferenceSets", "title": "searchReferenceSets function", "topics": [ "searchReferenceSets" ] }, { "page": "searchRnaQuantifications", "title": "searchRnaQuantifications function", "topics": [ "searchRnaQuantifications" ] }, { "page": "searchRnaQuantificationSets", "title": "searchRnaQuantificationSets function", "topics": [ "searchRnaQuantificationSets" ] }, { "page": "searchVariantAnnotations", "title": "searchVariantAnnotations function", "topics": [ "searchVariantAnnotations" ] }, { "page": "searchVariantAnnotationSets", "title": "searchVariantAnnotationSets function", "topics": [ "searchVariantAnnotationSets" ] }, { "page": "searchVariants", "title": "searchVariants function", "topics": [ "searchVariants" ] }, { "page": "searchVariantsByGRanges", "title": "searchVariantsByGranges function", "topics": [ "searchVariantsByGRanges" ] }, { "page": "searchVariantSets", "title": "searchVariantSets function", "topics": [ "searchVariantSets" ] } ], "_readme": "https://github.com/bioc/GA4GHclient/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "dplyr", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "tibble", "tidyselect", "utf8", "VariantAnnotation", "vctrs", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "GA4GHclient.Rmd", "filename": "GA4GHclient.html", "title": "GA4GHclient", "author": "Welliton Souza", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Available request methods", "Retrieving Thousand Genomes Project data through GA4GHclient package", "Search Variants by genomic location of genes", "VariantAnnotation classes", "Session Information" ], "created": "2017-03-27 08:07:28", "modified": "2025-07-22 16:17:54", "commits": 4 } ], "_score": 4.653212513775344, "_indexed": true, "_nocasepkg": "ga4ghclient", "_universes": [ "bioc", "wdesouza", "labbcb" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-07-03T21:38:53.000Z", "distro": "resolute", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/4451aff6322943b7bcfed65bcbf2f512161e2a8f6a8798d7a1d640244c3c89ea", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" }, { "r": "4.6.1", "os": "linux", "version": "1.37.0", "date": "2026-07-03T21:38:54.000Z", "distro": "resolute", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/47ee96c03c0c41da55cd0dfb10f130f779ce55ed4f310dbcb95ca531aa7f3ee3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-07-03T21:36:20.000Z", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/f25e37a1b8c40d618bdb36d0b087b806966f4154789c5a1bb3d5c3c4ac954114", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" }, { "r": "4.6.1", "os": "mac", "version": "1.37.0", "date": "2026-07-03T21:37:00.000Z", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/a4b6aa2496b236199f83154f9eec39ea77afc0c1caa8275134da6d844de9455f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.0", "date": "2026-07-03T21:38:51.000Z", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/af354f60240aa420398a309757cc2355d3d6d62d0e4dc5561be2a12d035cf3ea", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-07-03T21:37:02.000Z", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/ed312ea7132eabbf7adaed31a1e33c52307994e06a7b638d8efd12d9d3d061d0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-07-03T21:36:49.000Z", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/9fbeda78767f1bb3038282b166ea103573becff328dad30ca14d8f18483ead0e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" }, { "r": "4.6.1", "os": "win", "version": "1.37.0", "date": "2026-07-03T21:37:03.000Z", "commit": "7d0549e51e221273d102096a759fb0636296f991", "fileid": "https://r2.ropensci.org/39cd1fda21883469e2f788ff4b56768a0229da836cb9a665792921e5d906def0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684136088" } ] }