{ "_id": "6adb1230343c88418cb7293a", "Package": "seq2pathway", "Type": "Package", "Title": "a novel tool for functional gene-set (or termed as pathway)\nanalysis of next-generation sequencing data", "Version": "1.44.0", "Date": "2021-11-21", "Author": "Xinan Yang ; Bin Wang ", "Maintainer": "Arjun Kinstlick ", "biocViews": "Software", "Description": "Seq2pathway is a novel tool for functional gene-set (or\ntermed as pathway) analysis of next-generation sequencing data,\nconsisting of \"seq2gene\" and \"gene2path\" components. The\nseq2gene links sequence-level measurements of genomic regions\n(including SNPs or point mutation coordinates) to gene-level\nscores, and the gene2pathway summarizes gene scores to\npathway-scores for each sample. The seq2gene has the\nfeasibility to assign both coding and non-exon regions to a\nbroader range of neighboring genes than only the nearest one,\nthus facilitating the study of functional non-coding regions.\nThe gene2pathway takes into account the quantity of\nsignificance for gene members within a pathway compared those\noutside a pathway. The output of seq2pathway is a general\nstructure of quantitative pathway-level scores, thus allowing\none to functional interpret such datasets as RNA-seq, ChIP-seq,\nGWAS, and derived from other next generational sequencing\nexperiments.", "License": "GPL-2", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:40:28 UTC", "RemoteUrl": "https://github.com/bioc/seq2pathway", "RemoteRef": "RELEASE_3_23", "RemoteSha": "36eec067b33536614745d395bfa1372f0a822497", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-23 07:45:19 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "seq2pathway_1.44.0.tar.gz", "_fileid": "https://r2.ropensci.org/f05ca7a9f973a71e7ca7c8ca03316ddf938e5e5f7aa5a7ab029c7a225510833a", "_filesize": 1617900, "_sha256": "f05ca7a9f973a71e7ca7c8ca03316ddf938e5e5f7aa5a7ab029c7a225510833a", "_expires": "2027-01-31T07:52:14.000Z", "_created": "2026-10-23T07:45:19.000Z", "_published": "2026-10-23T07:52:16.690Z", "_upstream": "https://github.com/bioc/seq2pathway", "_status": "success", "_maintainer": { "name": "Arjun Kinstlick", "email": "akinstlick@uchicago.edu" }, "_jobs": [ { "job": 120302517694, "time": 170, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12486753649" }, { "job": 120302517708, "time": 346, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12487655132" }, { "job": 120302517621, "time": 365, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12485814125" }, { "job": 120302517748, "time": 264, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "12486708691" }, { "job": 120302517592, "time": 266, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12485809040" }, { "job": 120300220234, "time": 366, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12487111200" }, { "job": 120302517609, "time": 160, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12487281011" }, { "job": 120302517599, "time": 347, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12486583243" }, { "job": 120302517681, "time": 280, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12487575353" }, { "job": 120302517544, "time": 273, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12486767515" } ], "_bioccheck": { "error": 3, "warning": 5, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245", "_commit": { "id": "36eec067b33536614745d395bfa1372f0a822497", "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": 1777380028 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.2", "role": "Depends" }, { "package": "nnet", "role": "Imports" }, { "package": "WGCNA", "role": "Imports" }, { "package": "GSA", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "seq2pathway.data", "role": "Imports" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 622, "source": "https://www.bioconductor.org/packages/stats/bioc/seq2pathway" }, "_mentions": 1, "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/seq2pathway.html" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "addDescription", "FisherTest_GO_BP_MF_CC", "FisherTest_MsigDB", "gene2pathway_test", "plotTop10", "runseq2gene", "runseq2pathway" ], "_datasets": [ { "name": "Chipseq_Peak_demo", "title": "chip seq loci data example", "object": "Chipseq_Peak_demo", "file": "Chipseq_Peak_demo.rda", "class": [ "data.frame" ], "fields": [ "peakID", "chrom", "start", "end", "signalvalue" ], "rows": 5, "table": true, "tojson": true }, { "name": "dat_chip", "title": "chip seq data example", "object": "dat_chip", "file": "dat_chip.rda", "class": [ "data.frame" ], "fields": [ "peakscore" ], "rows": 639, "table": true, "tojson": true }, { "name": "dat_RNA", "title": "RNA sequence data example", "object": "dat_RNA", "file": "dat_RNA.rda", "class": [ "data.frame" ], "fields": [ "TCGA_2841", "TCGA_2840", "TCGA_2843", "TCGA_2842", "TCGA_2845" ], "rows": 5000, "table": true, "tojson": true }, { "name": "GRanges_demo", "title": "loci information with GRanges format", "object": "GRanges_demo", "file": "GRanges_demo.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "addDescription", "title": "Retrieve \"gene description\" attributes for gene symbol.", "topics": [ "addDescription" ] }, { "page": "Chipseq_Peak_demo", "title": "chip seq loci data example", "topics": [ "Chipseq_Peak_demo" ] }, { "page": "dat_chip", "title": "chip seq data example", "topics": [ "dat_chip" ] }, { "page": "dat_RNA", "title": "RNA sequence data example", "topics": [ "dat_RNA" ] }, { "page": "FisherTest_GO_BP_MF_CC", "title": "A wrapper function to perform the Fisher's exact test, using GO-defined genesets.", "topics": [ "FisherTest_GO_BP_MF_CC" ] }, { "page": "FisherTest_MsigDB", "title": "A wrapper function to perform conditional Fisher's exact test, using custom-defined genesets.", "topics": [ "FisherTest_MsigDB" ] }, { "page": "gene2pathway_test", "title": "A wrapper function to perform gene2pathway test.", "topics": [ "gene2pathway_test" ] }, { "page": "GRanges_demo", "title": "loci information with GRanges format", "topics": [ "GRanges_demo" ] }, { "page": "plotTop10", "title": "A wrapper function to plot top10 test results.", "topics": [ "plotTop10" ] }, { "page": "runseq2gene", "title": "R wrapped python function to map genomic regions on the sequence-level to genes.", "topics": [ "runseq2gene" ] }, { "page": "runseq2pathway", "title": "An function to perform the runseq2pathway algorithm(s).", "topics": [ "runseq2pathway" ] } ], "_readme": "https://github.com/bioc/seq2pathway/raw/RELEASE_3_23/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "backports", "base64enc", "Biobase", "BiocFileCache", "BiocGenerics", "biomaRt", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "checkmate", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "digest", "doParallel", "dplyr", "dynamicTreeCut", "evaluate", "farver", "fastcluster", "fastmap", "filelock", "fontawesome", "foreach", "foreign", "Formula", "fs", "generics", "GenomicRanges", "ggplot2", "glue", "gridExtra", "GSA", "gtable", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "memoise", "mime", "nnet", "openssl", "pillar", "pkgconfig", "png", "preprocessCore", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "rmarkdown", "rpart", "RSQLite", "rstudioapi", "S4Vectors", "S7", "sass", "scales", "seq2pathway.data", "Seqinfo", "stringi", "stringr", "survival", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "WGCNA", "withr", "xfun", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "seq2pathwaypackage.Rnw", "filename": "seq2pathwaypackage.pdf", "title": "An R package for sequence", "engine": "utils::Sweave", "headings": [ "Abstract", "Package Installation", "runseq2pathway", "Two main functions", "Examples", "R environment session" ], "created": "2015-01-14 21:22:07", "modified": "2021-06-08 18:32:30", "commits": 15 } ], "_score": 4, "_indexed": false, "_nocasepkg": "seq2pathway", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/seq2pathway", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.44.0", "date": "2026-10-23T07:48:23.000Z", "distro": "resolute", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/5f8378b651a2d19f98aee9086814f46d23cece255419bd285b6766f79ee7ba97", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" }, { "r": "4.6.1", "os": "linux", "version": "1.44.0", "date": "2026-10-23T07:49:11.000Z", "distro": "resolute", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/fdd98ef0a941e078d416734b575cd9c51d85572ad8eb917abbaa87f52942b816", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" }, { "r": "4.5.3", "os": "mac", "version": "1.44.0", "date": "2026-10-23T07:47:32.000Z", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/41902c37ddd6f147704789083bd46495204949ad3f9721bfd341987fd3220ea8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" }, { "r": "4.6.1", "os": "mac", "version": "1.44.0", "date": "2026-10-23T07:47:33.000Z", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/d419788704c60331a2a61e3533bda3e5586639e15737924842d0ee4e6acaa5aa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" }, { "r": "4.6.0", "os": "wasm", "version": "1.44.0", "date": "2026-10-23T07:48:21.000Z", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/ccc5a54cfad8880eb0789f1b8e73b4cd876bf08ec354d9f426e88396370d8bb4", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" }, { "r": "4.7.0", "os": "win", "version": "1.44.0", "date": "2026-10-23T07:47:24.000Z", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/17f41b0d573b9b944d6a436eb2b43da47c8d190482a150fc4c73532f4f12f83d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" }, { "r": "4.5.3", "os": "win", "version": "1.44.0", "date": "2026-10-23T07:47:02.000Z", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/5abcd5842cf79bdc872908ae8f4b603fa1454313f473fb9f52e9bf255670cb98", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" }, { "r": "4.6.1", "os": "win", "version": "1.44.0", "date": "2026-10-23T07:47:13.000Z", "commit": "36eec067b33536614745d395bfa1372f0a822497", "fileid": "https://r2.ropensci.org/971d7966eb4113060c588f4f8caf37d4645da1e3e1defce4d25f88373b7ae624", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/39919212245" } ] }