{ "_id": "6a1b04a81d7bb097a0a02924", "Package": "traseR", "Type": "Package", "Title": "GWAS trait-associated SNP enrichment analyses in genomic\nintervals", "Version": "1.42.0", "Date": "2021-11-21", "Author": "Li Chen, Zhaohui S.Qin", "Maintainer": "li chen", "Description": "traseR performs GWAS trait-associated SNP enrichment\nanalyses in genomic intervals using different hypothesis\ntesting approaches, also provides various functionalities to\nexplore and visualize the results.", "License": "GPL", "LazyLoad": "yes", "biocViews": "Genetics,Sequencing, Coverage, Alignment, QualityControl,\nDataImport", "NeedsCompilation": "no", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:41:33 UTC", "RemoteUrl": "https://github.com/bioc/traseR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "Packaged": { "Date": "2026-05-30 10:39:40 UTC", "User": "root" }, "MD5sum": "853fd8986112951c8311044b25ac8feb", "_user": "bioc-release", "_type": "src", "_file": "traseR_1.42.0.tar.gz", "_fileid": "52cf986a3540bd637c1ea26ef78da3307ce800ce96bd04a65a5d372b5a65f65d", "_filesize": 6635523, "_sha256": "52cf986a3540bd637c1ea26ef78da3307ce800ce96bd04a65a5d372b5a65f65d", "_created": "2026-05-30T10:39:40.000Z", "_published": "2026-05-30T15:39:20.729Z", "_jobs": [ { "job": 78643255783, "time": 241, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307674292" }, { "job": 78643255780, "time": 381, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307688451" }, { "job": 78643255779, "time": 342, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307683796" }, { "job": 78643255805, "time": 229, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309313041" }, { "job": 78643255800, "time": 237, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309316267" }, { "job": 78640902990, "time": 385, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307580753" }, { "job": 78643255769, "time": 188, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307669067" }, { "job": 78643255815, "time": 803, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307724563" }, { "job": 78643255819, "time": 751, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307719753" }, { "job": 78643255799, "time": 810, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307725132" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/traseR", "_commit": { "id": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380093 }, "_maintainer": { "name": "li chen", "email": "li.chen@emory.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "IRanges", "role": "Depends" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Depends" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.43.0", "bioc": "3.24" }, { "branch": "release", "version": "1.42.0", "bioc": "3.23" } ], "_topics": [ "genetics", "sequencing", "coverage", "alignment", "qualitycontrol", "dataimport" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 416, "source": "https://www.bioconductor.org/packages/stats/bioc/traseR" }, "_mentions": 1, "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/traseR.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "plotContext", "plotGene", "plotInterval", "plotPvalue", "plotSNP", "print.traseR", "queryGene", "queryKeyword", "querySNP", "traseR" ], "_datasets": [ { "name": "CEU", "title": "Sampled SNPs from all SNPs of CEU population in 1000 genome project", "object": "CEU", "file": "CEU.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "taSNP", "title": "trait-associated SNPs in dbGaP and NHGRI downloaded from Association Results Browser", "object": "taSNP", "file": "taSNP.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "taSNPLD", "title": "linkage disequilibrium (>0.8) within 100kb SNPs of all trait-associated SNPs from dbGaP and NHGRI", "object": "taSNPLD", "file": "taSNPLD.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "Tcell", "title": "Peak regions of H3K4me1 in Peripheral blood T cell", "object": "Tcell", "file": "Tcell.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "traseR-package", "title": "GWAS trait-associated SNP enrichment analyses in genomic intervals", "topics": [ "traseR-package" ] }, { "page": "CEU", "title": "Sampled SNPs from all SNPs of CEU population in 1000 genome project", "topics": [ "CEU" ] }, { "page": "plots", "title": "Visualize of trait-associated SNPs", "topics": [ "plotContext", "plotGene", "plotInterval", "plotPvalue", "plotSNP" ] }, { "page": "print.traseR", "title": "Print the outcome of taSNP enrichment analyses", "topics": [ "print.traseR" ] }, { "page": "querys", "title": "Retrieve trait-associated SNPs based", "topics": [ "queryGene", "queryKeyword", "querySNP" ] }, { "page": "taSNP", "title": "trait-associated SNPs in dbGaP and NHGRI downloaded from Association Results Browser", "topics": [ "taSNP" ] }, { "page": "taSNPLD", "title": "linkage disequilibrium (>0.8) within 100kb SNPs of all trait-associated SNPs from dbGaP and NHGRI", "topics": [ "taSNPLD" ] }, { "page": "Tcell", "title": "Peak regions of H3K4me1 in Peripheral blood T cell", "topics": [ "Tcell" ] }, { "page": "traseR", "title": "TRait-Associated SNP EnRichment analyses", "topics": [ "traseR" ] } ], "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "BSgenome", "BSgenome.Hsapiens.UCSC.hg19", "cigarillo", "codetools", "cpp11", "crayon", "curl", "DelayedArray", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "httr", "IRanges", "jsonlite", "lambda.r", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "traseR.Rnw", "filename": "traseR.pdf", "title": "Perform GWAS trait-associated SNP enrichment analyses in genomic intervals", "engine": "utils::Sweave", "headings": [], "created": "2015-07-16 19:09:19", "modified": "2015-11-20 23:33:18", "commits": 4 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "traser", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/traseR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.42.0", "date": "2026-05-30T10:56:06.000Z", "distro": "noble", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "545c122f41dded587aa77b7dbc9f6bedbd8dd1a476e49a461009eb15bdbcaefe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" }, { "r": "4.6.0", "os": "linux", "version": "1.42.0", "date": "2026-05-30T10:55:14.000Z", "distro": "noble", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "9b1c6458f87b80423083fa96d153d41f5f030d05099b38ecd878710058d10018", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" }, { "r": "4.5.3", "os": "mac", "version": "1.42.0", "date": "2026-05-30T15:36:33.000Z", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "729a1f5fefca30b02af83954b646cfb2feb6a261fc4a1cfb4fb98276d4569125", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" }, { "r": "4.6.0", "os": "mac", "version": "1.42.0", "date": "2026-05-30T15:37:01.000Z", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "34f57d0505d0114782fa336bcfe26438584dd21eb07c00593718e5bddcc07279", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" }, { "r": "4.6.0", "os": "wasm", "version": "1.42.0", "date": "2026-05-30T10:55:16.000Z", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "81f5becb9106412b6ab22dcd60c63bc43c56c10d710d5a2232d43ce4391c2e0a", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" }, { "r": "4.7.0", "os": "win", "version": "1.42.0", "date": "2026-05-30T11:02:04.000Z", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "b291596444139e488d9258e53fca80b99f49c66f7e5bebfff4b033b214705c69", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" }, { "r": "4.5.3", "os": "win", "version": "1.42.0", "date": "2026-05-30T11:01:12.000Z", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "c958d45fa4c1b6d2199ae8888395b1055d4c4dc9d41f1e94f57db9eda055b79c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" }, { "r": "4.6.0", "os": "win", "version": "1.42.0", "date": "2026-05-30T11:02:00.000Z", "commit": "89fe4aad0fe03a92079812a6d17cb5b48fefa423", "fileid": "38ca76618588261493d5e24876c544ec52930179c690acf0e48ae9823e81036a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680426989" } ] }