{ "_id": "6aedd90e818c9e3ef6dc4796", "Package": "GPlinksR", "Type": "Package", "Title": "Building Gene-Peak Network for ATAC-RNA Integration", "Version": "0.99.2", "Authors@R": "c(\nperson(\n\"Xinran\", \"Wang\",\nemail = \"xwang210@usc.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-1805-3280\")\n),\nperson(\"Kelly\", \"Street\", email = \"kelly.street@usc.edu\", role = \"ctb\"),\nperson(\"Huaiyu\", \"Mi\", email = \"huaiyumi@usc.edu\", role = \"ctb\"),\nperson(\"Bryan\", \"Queme\", email = \"queme@usc.edu\", role = \"ctb\"))", "Description": "GPlinksR constructs gene-peak regulatory networks for\nATAC-RNA integration by combining enhancer-based,\npromoter-based, and proximity (closest-gene) mappings. The\npackage accepts direct peak and gene vectors as well as\ncontainer-based inputs through a wrapper for common\nBioconductor object classes. Enhancer-gene links are obtained\nfrom the PEREGRINE enhancer-gene datasets provided by AnnoQ,\nwhile promoter and gene coordinates are retrieved from\nEnsDb.Hsapiens.v86.", "License": "MIT + file LICENSE", "URL": "https://github.com/Corawang123/GPlinksR", "BugReports": "https://github.com/Corawang123/GPlinksR/issues", "Encoding": "UTF-8", "biocViews": "GeneExpression, Network, Sequencing, Transcriptomics", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-14 21:00:04 UTC", "RemoteUrl": "https://github.com/bioc/GPlinksR", "RemoteRef": "HEAD", "RemoteSha": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-06 13:35:15 UTC", "User": "root" }, "Author": "Xinran Wang [aut, cre] (ORCID: ),\nKelly Street [ctb],\nHuaiyu Mi [ctb],\nBryan Queme [ctb]", "Maintainer": "Xinran Wang ", "_user": "bioc", "_type": "src", "_file": "GPlinksR_0.99.2.tar.gz", "_fileid": "https://r2.ropensci.org/dc0b0ca8572fb718c9d6d2d7ab7b036b0caa98893acaa66fee762c550785634b", "_filesize": 133338, "_sha256": "dc0b0ca8572fb718c9d6d2d7ab7b036b0caa98893acaa66fee762c550785634b", "_expires": "2027-02-14T13:41:32.000Z", "_created": "2026-11-06T13:35:15.000Z", "_published": "2026-11-06T13:41:33.860Z", "_upstream": "https://github.com/bioc/GPlinksR", "_status": "success", "_maintainer": { "name": "Xinran Wang", "email": "xwang210@usc.edu", "login": "corawang123", "description": "", "uuid": 122309888, "orcid": "0009-0000-1805-3280" }, "_jobs": [ { "job": 127922032813, "time": 193, "config": "bioc-checks", "r": "4.6.2", "check": "OK", "artifact": "13506421657" }, { "job": 127922032688, "time": 322, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13505444918" }, { "job": 127922032619, "time": 338, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13505449743" }, { "job": 127922033145, "time": 246, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13505478443" }, { "job": 127922032453, "time": 185, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13506192013" }, { "job": 127920075361, "time": 253, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13505314234" }, { "job": 127922032436, "time": 138, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13505244753" }, { "job": 127922032980, "time": 196, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13506197454" }, { "job": 127922032554, "time": 152, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13505677771" }, { "job": 127922032727, "time": 201, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13505738848" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 0 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930", "_commit": { "id": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "author": "Corawang123 ", "committer": "Corawang123 ", "message": "Synchronize personal and BiocStaging histories\n", "time": 1784062804 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "EnsDb.Hsapiens.v86", "role": "Imports" }, { "package": "ensembldb", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-49", "n": 3 }, { "week": "2025-51", "n": 1 }, { "week": "2026-09", "n": 2 }, { "week": "2026-10", "n": 1 }, { "week": "2026-13", "n": 2 }, { "week": "2026-16", "n": 1 }, { "week": "2026-19", "n": 1 }, { "week": "2026-21", "n": 3 }, { "week": "2026-26", "n": 2 }, { "week": "2026-29", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "0.99.2", "bioc": "3.24", "repository": "bioc", "r": "4.6.0" } ], "_topics": [ "geneexpression", "network", "sequencing", "transcriptomics" ], "_stars": 0, "_contributors": [ { "user": "corawang123", "count": 20, "uuid": 122309888 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 485, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 412, "source": "https://www.bioconductor.org/packages/stats/bioc/GPlinksR" }, "_devurl": "https://github.com/corawang123/gplinksr", "_searchresults": 3, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GPlinksR.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/corawang123/gplinksr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "build_gp_links", "build_gp_links_wrapper", "get_peregrine_file" ], "_datasets": [ { "name": "gp_example_inputs", "title": "Example Gene and Peak Inputs for GPlinksR", "object": "gp_example_inputs", "file": "gp_example_inputs.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "gp_example_links", "title": "Example Link Table for the Packaged GPlinksR Demo Subset", "object": "gp_example_links", "file": "gp_example_links.rda", "class": [ "data.frame" ], "fields": [ "Peak", "Gene", "Src" ], "rows": 7, "table": true, "tojson": true } ], "_help": [ { "page": "build_gp_links", "title": "Build Gene-Peak Network (Enhancer, Promoter, Closest)", "topics": [ "build_gp_links" ] }, { "page": "build_gp_links_wrapper", "title": "Build Gene-Peak Links from MAE or SCE Input", "topics": [ "build_gp_links_wrapper" ] }, { "page": "get_peregrine_file", "title": "Download Enhancer-Gene Link File from PANTHER Peregrine Database", "topics": [ "get_peregrine_file" ] }, { "page": "gp_example_inputs", "title": "Example Gene and Peak Inputs for GPlinksR", "topics": [ "gp_example_inputs" ] }, { "page": "gp_example_links", "title": "Example Link Table for the Packaged GPlinksR Demo Subset", "topics": [ "gp_example_links" ] } ], "_readme": "https://github.com/bioc/GPlinksR/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "digest", "dplyr", "EnsDb.Hsapiens.v86", "ensembldb", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "hms", "httr", "httr2", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lazyeval", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "MultiAssayExperiment", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ProtGenerics", "purrr", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "UCSC.utils", "utf8", "vctrs", "withr", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "GPlinksR.Rmd", "filename": "GPlinksR.html", "title": "GPlinksR: Building Gene-Peak Links from Example Single-Cell Inputs", "author": "Xinran Wang, Kelly Street, Huaiyu Mi, and Bryan Queme", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Overview", "Minimal Example with Real Peak and Gene Vectors", "Using a Peak Data Frame", "Wrapper Workflow for MultiAssayExperiment", "Wrapper Workflow for SingleCellExperiment", "Input Expectations", "Session Info" ], "created": "2026-03-27 23:00:44", "modified": "2026-07-14 20:54:32", "commits": 3 } ], "_score": 4.698970004336019, "_indexed": true, "_nocasepkg": "gplinksr", "_universes": [ "bioc", "corawang123" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.2", "date": "2026-11-06T13:39:45.000Z", "distro": "resolute", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/9df45c69b27e5718b107e1538699f1c260bd0977af5e42290e25447258943685", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" }, { "r": "4.6.2", "os": "linux", "version": "0.99.2", "date": "2026-11-06T13:40:06.000Z", "distro": "resolute", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/12a9b157eff76b528e14a0057838ed404eea62ff3d36d542e8d9c59eeaf6f137", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" }, { "r": "4.5.3", "os": "mac", "version": "0.99.2", "date": "2026-11-06T13:38:10.000Z", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/43f2860adb8e620760ea0876fc25b1d104202cffe2b5e1fa3ee71785bf57ecf2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" }, { "r": "4.6.2", "os": "mac", "version": "0.99.2", "date": "2026-11-06T13:37:36.000Z", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/d2f203917ff5e3f21ac514d8b621c13447bf140723cb067ee250187202596e0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.2", "date": "2026-11-06T13:37:50.000Z", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/e68842f4f1f4537567526167020f2860cdedbb3d625080a47a829366a3fc89a2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" }, { "r": "4.7.0", "os": "win", "version": "0.99.2", "date": "2026-11-06T13:37:37.000Z", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/c2a569d70483d778ab4f8defcc8c50b0e94be280836003585e05e6e94695d183", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" }, { "r": "4.5.3", "os": "win", "version": "0.99.2", "date": "2026-11-06T13:37:10.000Z", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/4e04505d38cf7ffdc5e5cae11662e08c2f481f1f91c779f297db01cd9980fc20", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" }, { "r": "4.6.2", "os": "win", "version": "0.99.2", "date": "2026-11-06T13:37:26.000Z", "commit": "6a7555bbae86bfc5e04abcd975f8b200a606efc2", "fileid": "https://r2.ropensci.org/a69162d622a8ccda2d18be2f05af55f9a7b7d00bc91b07a20161b25272f1025d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/42226121930" } ] }