{ "_id": "6a1c06f41d7bb097a0a2b6d5", "Package": "PCSF", "Type": "Package", "Title": "Network-based interpretation of highthroughput data", "Version": "0.99.1", "Date": "2017-02-01", "Author": "Murodzhon Akhmedov, Amanda Kedaigle, Renan Escalante, Roberto\nMontemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee", "Maintainer": "Murodzhon Akhmedov ", "Description": "The PCSF package performs an integrated analysis of\nhighthroughput data using the interaction networks as a\ntemplate, and interprets the biological landscape of\ninteraction networks with respect to the data, which\npotentially leads to predictions of functional units. It also\ninteractively visualize the resulting subnetwork with\nfunctional enrichment analysis.", "License": "MIT + file LICENSE", "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "cmake libglpk-dev make libpng-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://cogdisreslab.r-universe.dev", "Date/Publication": "2019-05-07 09:02:15 UTC", "RemoteUrl": "https://github.com/CogDisResLab/PCSF", "RemoteRef": "HEAD", "RemoteSha": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-31 09:51:24 UTC", "User": "root" }, "MD5sum": "90ef11ea1fe015567077a448176de9b2", "_user": "cogdisreslab", "_type": "src", "_file": "PCSF_0.99.1.tar.gz", "_fileid": "0b52e4616b2aced0c78d434c4411bfde0cbcffd466315e572f8e14aa0e1b3bfa", "_filesize": 1837749, "_sha256": "0b52e4616b2aced0c78d434c4411bfde0cbcffd466315e572f8e14aa0e1b3bfa", "_created": "2026-05-31T09:51:24.000Z", "_published": "2026-05-31T10:01:23.995Z", "_distro": "noble", "_jobs": [ { "job": 78716627046, "time": 250, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7315766039" }, { "job": 78716627013, "time": 243, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7315765155" }, { "job": 78716627042, "time": 237, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7315764634" }, { "job": 78716627044, "time": 250, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7315766068" }, { "job": 78716627056, "time": 195, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7315765266" }, { "job": 78716627062, "time": 379, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7315788409" }, { "job": 78716627045, "time": 134, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7315759596" }, { "job": 78716627031, "time": 384, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7315784914" }, { "job": 78716399706, "time": 249, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7315740467" }, { "job": 78716627025, "time": 184, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7315758809" }, { "job": 78716627018, "time": 545, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7315799290" }, { "job": 78716627022, "time": 498, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7315793627" }, { "job": 78716627024, "time": 227, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7315763418" } ], "_buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/CogDisResLab/PCSF", "_commit": { "id": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "author": "murodzhon ", "committer": "GitHub ", "message": "Update README.md", "time": 1557219735 }, "_maintainer": { "name": "Murodzhon Akhmedov", "email": "murodzhon@idsia.ch" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.0", "role": "Depends" }, { "package": "igraph", "role": "Depends" }, { "package": "visNetwork", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "BH", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "topGO", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cogdisreslab", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "murodzhon", "count": 51, "uuid": 20000070 }, { "user": "ivokwee", "count": 1, "uuid": 19613146 } ], "_userbio": { "uuid": 83421213, "type": "organization", "name": "Cognitive Disorders Research Lab" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PCSF" }, "_devurl": "https://github.com/cogdisreslab/pcsf", "_searchresults": 94, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PCSF.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "call_enr", "call_sr", "construct_interactome", "enrichment_analysis", "PCSF", "PCSF_rand", "plot.PCSF", "plot.PCSFe" ], "_datasets": [ { "name": "STRING", "title": "Protein-protein interaction network data", "object": "STRING", "file": "STRING.rda", "class": [ "data.frame" ], "fields": [ "from", "to", "cost" ], "rows": 175854, "table": true, "tojson": true }, { "name": "Tgfb_phospho", "title": "Phosphoproteomic data", "object": "Tgfb_phospho", "file": "Tgfb_phospho.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "construct_interactome", "title": "Construct an interaction network", "topics": [ "construct_interactome" ] }, { "page": "enrichment_analysis", "title": "Perform enrichment analysis on the subnetwork", "topics": [ "enrichment_analysis" ] }, { "page": "PCSF", "title": "Prize-collecting Steiner Forest (PCSF)", "topics": [ "PCSF" ] }, { "page": "PCSF_rand", "title": "Prize-collecting Steiner Forest (PCSF) with randomized edge costs", "topics": [ "PCSF_rand" ] }, { "page": "plot.PCSF", "title": "Plot an interactive subnetwork", "topics": [ "plot.PCSF" ] }, { "page": "plot.PCSFe", "title": "Plot an interactive subnetwork with functional enrichment analysis", "topics": [ "plot.PCSFe" ] }, { "page": "STRING", "title": "Protein-protein interaction network data", "topics": [ "STRING" ] }, { "page": "Tgfb_phospho", "title": "Phosphoproteomic data", "topics": [ "Tgfb_phospho" ] } ], "_readme": "https://github.com/CogDisResLab/PCSF/raw/HEAD/README.md", "_rundeps": [ "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "digest", "evaluate", "fastmap", "fontawesome", "fs", "generics", "glue", "GO.db", "graph", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "IRanges", "jquerylib", "jsonlite", "KEGGREST", "knitr", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "memoise", "mime", "openssl", "org.Hs.eg.db", "pkgconfig", "png", "R6", "rappdirs", "Rcpp", "rlang", "rmarkdown", "RSQLite", "S4Vectors", "sass", "Seqinfo", "SparseM", "sys", "tinytex", "topGO", "vctrs", "visNetwork", "xfun", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 3.1492191126553797, "_indexed": true, "_nocasepkg": "pcsf", "_universes": [ "cogdisreslab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-05-31T09:54:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "4d759e06ff03e07907cbcddd0a52153bc141f25f476da03744d8463ea5c02361", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-05-31T09:54:36.000Z", "distro": "noble", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "df58027e27b1c879554f54fb404d5165af117899433ccf2e7856aa2e7a413acd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.6.0", "os": "linux", "version": "0.99.1", "date": "2026-05-31T09:54:40.000Z", "distro": "noble", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "7c24144c7db7b3c0854d308a2a6a31096ca464cab3783e3a46f66886ec6a6997", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.6.0", "os": "linux", "version": "0.99.1", "date": "2026-05-31T09:54:43.000Z", "distro": "noble", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "3f7c3c13b4176f2fd3bddde138f590fd4d4a6ec562ecafee70e0fa21f06f4e5e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-05-31T09:54:30.000Z", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "966bb56229f6e58db17f05011216f6e1f659fd05b43d6b73b1c7e106b6abc478", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-05-31T09:57:15.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "b401203a68fe996bbe5f1e3d78013003d2e6a98706ea2176bdb28c8e39f3b6d5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.6.0", "os": "mac", "version": "0.99.1", "date": "2026-05-31T09:54:18.000Z", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "95b1da49a67ce547d9e93565891f5776b00ba1c6bb1bf2d19d7505ee42454de1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.6.0", "os": "mac", "version": "0.99.1", "date": "2026-05-31T09:56:22.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "bdbeb662dd6dbc9b8e982c82aa44452ca99661251588ea7da2483965fff19b61", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.1", "date": "2026-05-31T09:54:53.000Z", "arch": "emscripten", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "ecc69ec27e67f0edd496301441b8ec9fece28ab5629e8a0f0a7ba18de0f48b3c", "status": "success", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.7.0", "os": "win", "version": "0.99.1", "date": "2026-05-31T09:59:18.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "5fbb140ce5b19f3c450cb8669ccce2f79ce59f3925c372d4f8d95aa696c84df1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.5.3", "os": "win", "version": "0.99.1", "date": "2026-05-31T09:58:29.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "302041c5218ebfaf0990a7623aed46b91f7c274e88034b7f93885eea61bd99e0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" }, { "r": "4.6.0", "os": "win", "version": "0.99.1", "date": "2026-05-31T09:53:46.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "b3e5804b3255ee38ea70081c287ddc17cc06778861a604f97fdb52937ce4bdd8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/26709295537" } ] }