{ "_id": "6a1af4df1d7bb097a09f8e7c", "Package": "systemPipeShiny", "Title": "systemPipeShiny: An Interactive Framework for Workflow\nManagement and Visualization", "Version": "1.23.0", "Date": "2025-05-19", "Authors@R": "c(\nperson(given = \"Le\", family = \"Zhang\", role = c(\"aut\", \"cre\"), email = \"le.zhang001@email.ucr.edu\"),\nperson(given = \"Daniela\", family = \"Cassol\", role = c(\"aut\"), email = \"danicassol@gmail.com\"),\nperson(given = \"Ponmathi\", family = \"Ramasamy\", role = c(\"aut\"), email = \"prama008@ucr.edu\"),\nperson(given = \"Jianhai\", family = \"Zhang\", role = c(\"aut\"), email = \"jzhan067@ucr.edu\"),\nperson(given = \"Gordon\", family = \"Mosher\", role = c(\"aut\"), email = \"gmosh001@ucr.edu\"),\nperson(given = \"Thomas\", family = \"Girke\", role = c(\"aut\"), email = \"thomas.girke@ucr.edu\"))", "Description": "systemPipeShiny (SPS) extends the widely used systemPipeR\n(SPR) workflow environment with a versatile graphical user\ninterface provided by a Shiny App. This allows non-R users,\nsuch as experimentalists, to run many systemPipeR’s workflow\ndesigns, control, and visualization functionalities\ninteractively without requiring knowledge of R. Most\nimportantly, SPS has been designed as a general purpose\nframework for interacting with other R packages in an intuitive\nmanner. Like most Shiny Apps, SPS can be used on both local\ncomputers as well as centralized server-based deployments that\ncan be accessed remotely as a public web service for using\nSPR’s functionalities with community and/or private data. The\nframework can integrate many core packages from the\nR/Bioconductor ecosystem. Examples of SPS’ current\nfunctionalities include: (a) interactive creation of\nexperimental designs and metadata using an easy to use tabular\neditor or file uploader; (b) visualization of workflow\ntopologies combined with auto-generation of R Markdown preview\nfor interactively designed workflows; (d) access to a wide\nrange of data processing routines; (e) and an extendable set of\nvisualization functionalities. Complex visual results can be\nmanaged on a 'Canvas Workbench’ allowing users to organize and\nto compare plots in an efficient manner combined with a session\nsnapshot feature to continue work at a later time. The present\nsuite of pre-configured visualization examples. The modular\ndesign of SPR makes it easy to design custom functions without\nany knowledge of Shiny, as well as extending the environment in\nthe future with contributions from the community.", "VignetteBuilder": "knitr", "biocViews": "ShinyApps, Infrastructure, DataImport, Sequencing,\nQualityControl, ReportWriting, ExperimentalDesign, Clustering", "License": "GPL (>= 3)", "Encoding": "UTF-8", "BugReports": "https://github.com/systemPipeR/systemPipeShiny/issues", "URL": "https://systempipe.org/sps,\nhttps://github.com/systemPipeR/systemPipeShiny", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:51 UTC", "RemoteUrl": "https://github.com/bioc/systemPipeShiny", "RemoteRef": "HEAD", "RemoteSha": "e0683c22a8c0478b92d17a111ec07a66f5228e0b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:46:01 UTC", "User": "root" }, "Author": "Le Zhang [aut, cre],\nDaniela Cassol [aut],\nPonmathi Ramasamy [aut],\nJianhai Zhang [aut],\nGordon Mosher [aut],\nThomas Girke [aut]", "Maintainer": "Le Zhang ", "MD5sum": "e309b2aaed83ce5de4c6bfc5e9248d4a", "_user": "bioc", "_type": "src", "_file": "systemPipeShiny_1.23.0.tar.gz", "_fileid": "bb664787900741cc66f2b14dfba4dcb571993d0e1f6d3b889fd01aedff97f133", "_filesize": 4397941, "_sha256": "bb664787900741cc66f2b14dfba4dcb571993d0e1f6d3b889fd01aedff97f133", "_created": "2026-05-30T09:46:01.000Z", "_published": "2026-05-30T14:31:59.594Z", "_jobs": [ { "job": 78640573472, "time": 236, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307479234" }, { "job": 78640573515, "time": 333, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307487555" }, { "job": 78640573470, "time": 319, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307486387" }, { "job": 78640573471, "time": 213, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308888884" }, { "job": 78640573478, "time": 147, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308881041" }, { "job": 78639831285, "time": 305, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307284493" }, { "job": 78640573461, "time": 206, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307476759" }, { "job": 78640573513, "time": 210, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307475850" }, { "job": 78640573503, "time": 218, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307476568" }, { "job": 78640573508, "time": 215, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307476491" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 19 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676764336", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/systemPipeShiny", "_commit": { "id": "e0683c22a8c0478b92d17a111ec07a66f5228e0b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380831 }, "_maintainer": { "name": "Le Zhang", "email": "le.zhang001@email.ucr.edu", "login": "lz100", "description": "Data engineer/scientist with expertise in bioinformatics data pipeline automation, visualization, and web application development. 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