{ "_id": "6a1ac0c01d7bb097a09d719d", "Package": "PAST", "Type": "Package", "Title": "Pathway Association Study Tool (PAST)", "Version": "1.29.0", "Authors@R": "c(person(\"Thrash\", \"Adam\", email = \"thrash@igbb.msstate.edu\",\nrole = c(\"cre\", \"aut\")), person(\"DeOrnellis\", \"Mason\", role = c(\"aut\")))", "Description": "PAST takes GWAS output and assigns SNPs to genes, uses\nthose genes to find pathways associated with the genes, and\nplots pathways based on significance. Implements methods for\nreading GWAS input data, finding genes associated with SNPs,\ncalculating enrichment score and significance of pathways, and\nplotting pathways.", "License": "GPL (>=3) + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.0", "URL": "https://github.com/IGBB/past", "BugReports": "https://github.com/IGBB/past/issues", "biocViews": "Pathways, GeneSetEnrichment", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:17 UTC", "RemoteUrl": "https://github.com/bioc/PAST", "RemoteRef": "HEAD", "RemoteSha": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:17:15 UTC", "User": "root" }, "Author": "Thrash Adam [cre, aut],\nDeOrnellis Mason [aut]", "Maintainer": "Thrash Adam ", "MD5sum": "23ff50b2e1afd1b129ea5f4d78765d79", "_user": "bioc", "_type": "src", "_file": "PAST_1.29.0.tar.gz", "_fileid": "934df55d1c2a872e5f2aaaf490f96d2cb463eeaa914cca90f53c74fe16fcfeab", "_filesize": 1069296, "_sha256": "934df55d1c2a872e5f2aaaf490f96d2cb463eeaa914cca90f53c74fe16fcfeab", "_created": "2026-05-30T07:17:15.000Z", "_published": "2026-05-30T10:49:36.932Z", "_jobs": [ { "job": 78632950204, "time": 185, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306419340" }, { "job": 78632950263, "time": 547, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306458831" }, { "job": 78632950203, "time": 482, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306450994" }, { "job": 78632950259, "time": 293, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307510503" }, { "job": 78632950262, "time": 317, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307518685" }, { "job": 78632653836, "time": 332, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306397691" }, { "job": 78632950198, "time": 160, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306416492" }, { "job": 78632950258, "time": 416, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306443537" }, { "job": 78632950265, "time": 427, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306444677" }, { "job": 78632950255, "time": 461, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306448573" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PAST", "_commit": { "id": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380617 }, "_maintainer": { "name": "Thrash Adam", "email": "thrash@igbb.msstate.edu", "login": "adamthrash", "description": "", "uuid": 1187214 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "iterators", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "pathways", "genesetenrichment" ], "_stars": 5, "_contributors": [ { "user": "adamthrash", "count": 15, "uuid": 1187214 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 376, "source": "https://www.bioconductor.org/packages/stats/bioc/PAST" }, "_mentions": 2336, "_devurl": "https://github.com/igbb/past", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PAST.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "assign_SNPs_to_genes", "find_pathway_significance", "load_GWAS_data", "load_LD", "plot_pathways" ], "_help": [ { "page": "assign_chunk", "title": "Assign SNPs in a chunk to genes", "topics": [ "assign_chunk" ] }, { "page": "assign_SNPs_to_genes", "title": "Assign SNPs to genes", "topics": [ "assign_SNPs_to_genes" ] }, { "page": "determine_linkage", "title": "Determine Linkage", "topics": [ "determine_linkage" ] }, { "page": "find_pathway_significance", "title": "Find Pathway Significance", "topics": [ "find_pathway_significance" ] }, { "page": "find_representative_SNP", "title": "Find representative SNP for a chunk of SNPs", "topics": [ "find_representative_SNP" ] }, { "page": "find_representative_SNP_gene_pairing", "title": "Find the SNP-gene assignment that represents SNPs assigned to a gene", "topics": [ "find_representative_SNP_gene_pairing" ] }, { "page": "load_GWAS_data", "title": "Load GWAS data", "topics": [ "load_GWAS_data" ] }, { "page": "load_LD", "title": "Load Linkage Disequilibrium", "topics": [ "load_LD" ] }, { "page": "plot_pathways", "title": "Plot Rugplots for Selected Pathways", "topics": [ "plot_pathways" ] } ], "_readme": "https://github.com/bioc/PAST/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DelayedArray", "doParallel", "dplyr", "farver", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "httr", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "pillar", "pkgconfig", "plyr", "qvalue", "R6", "RColorBrewer", "Rcpp", "RCurl", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "past.Rmd", "filename": "past.html", "title": "PAST", "author": "Adam Thrash", "engine": "knitr::rmarkdown", "headings": [ "PAST", "Loading GWAS Data", "Loading LD Data", "Assigning SNPs to Genes", "Finding Pathway Significance", "Plotting Selected Pathways", "References" ], "created": "2019-03-01 16:49:10", "modified": "2020-03-11 19:23:19", "commits": 9 } ], "_score": 5.698970004336019, "_indexed": true, "_nocasepkg": "past", "_universes": [ "bioc", "adamthrash", "igbb" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T07:21:31.000Z", "distro": "noble", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "3c8b17ae4f10f89031e5d7ec0a27a7d76b2eb8a9ac03430f8b2ee59c5b8389d9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" }, { "r": "4.6.0", "os": "linux", "version": "1.29.0", "date": "2026-05-30T07:20:39.000Z", "distro": "noble", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "68d245aa8394139ff0e4d13952637ef7603606e07bc084aa79c33387c6897de6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-05-30T10:24:00.000Z", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "b5b6f3c19ea4d17ddaa7f104ebb394fd5584bddbf2f7d0f05cf9b4363a1b21a4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" }, { "r": "4.6.0", "os": "mac", "version": "1.29.0", "date": "2026-05-30T10:25:27.000Z", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "67565a9ce87a986fa4728d563f232a41e067f941ee613d947e489fb4b413108c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-05-30T07:20:30.000Z", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "c3599c7641900776374c5bb802ed777d4e59153fa5c587bf912b110e31c50df1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-05-30T07:19:53.000Z", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "d90a78cc30de643b92fe5a01675b788e06cb3280daa482626682453a77bd52ed", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-05-30T07:19:28.000Z", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "8dc5c0e062e5e404147358ce18d4828cc7e08c0a90d9d6a201be4c814c081245", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" }, { "r": "4.6.0", "os": "win", "version": "1.29.0", "date": "2026-05-30T07:19:11.000Z", "commit": "b3a609543dc3cc58661b0b707e8a861b37a945b7", "fileid": "606103c95c7607de49eba7d614c1dfd59b21d88798c4d45b69ada34edd5ccaea", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677754237" } ] }