{ "_id": "6accdbd5a14063b82c3a9f15", "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": "2026-10-12 13:00:14 UTC", "User": "root" }, "_user": "cogdisreslab", "_type": "src", "_file": "PCSF_0.99.1.tar.gz", "_fileid": "https://r2.ropensci.org/0b1f51ad4bbe423c691f5defc1ac6e3cfbe45d5eb716f4dbe846e45fd92e422d", "_filesize": 1836946, "_sha256": "0b1f51ad4bbe423c691f5defc1ac6e3cfbe45d5eb716f4dbe846e45fd92e422d", "_expires": "2027-01-20T13:08:35.000Z", "_created": "2026-10-12T13:00:14.000Z", "_published": "2026-10-12T13:08:37.640Z", "_buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114822900055, "time": 255, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11749127345" }, { "job": 114822900080, "time": 244, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11749072329" }, { "job": 114822900265, "time": 216, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11748633218" }, { "job": 114822900253, "time": 182, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11749032143" }, { "job": 114822899964, "time": 198, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11748233301" }, { "job": 114822900170, "time": 295, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11748258169" }, { "job": 114822899990, "time": 209, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11749127229" }, { "job": 114822900445, "time": 426, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11748853224" }, { "job": 114821462399, "time": 224, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11748782036" }, { "job": 114822899900, "time": 152, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11749505349" }, { "job": 114822900125, "time": 443, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11749541058" }, { "job": 114822900085, "time": 258, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11748967318" }, { "job": 114822900247, "time": 205, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11749122306" }, { "job": 114822900134, "time": 444, "config": "windows-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11749207649" }, { "job": 114822900074, "time": 216, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11749122332" } ], "_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" }, "_distro": "resolute", "_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", "followers": 7 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PCSF" }, "_devurl": "https://github.com/cogdisreslab/pcsf", "_searchresults": 82, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/PCSF.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_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", "BiocBaseUtils", "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": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 3.089905111439398, "_indexed": true, "_nocasepkg": "pcsf", "_universes": [ "cogdisreslab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-10-12T13:03:44.000Z", "distro": "resolute", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/08a77cf56b1fbd34f167e1d445e57ac121af77ac22f97c6c010866eb67144edc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.7.0", "os": "linux", "version": "0.99.1", "date": "2026-10-12T13:03:20.000Z", "distro": "resolute", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/6e6b58c06ee0446d0dbc168d6b5c624542201e267007b7811bdfce669497f7cc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.6.1", "os": "linux", "version": "0.99.1", "date": "2026-10-12T13:03:15.000Z", "distro": "resolute", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/1330c5150b6220bff1bbd700f6a7ea40a8b1a48f50a4488b9f0e657758ba2ed3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.6.1", "os": "linux", "version": "0.99.1", "date": "2026-10-12T13:02:54.000Z", "distro": "resolute", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/245f4c0358973a2e823ac04767914ccf64bd9b0c879af16d8980846b2c973296", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-10-12T13:02:51.000Z", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/4ec1b29fa2df630895216ef345e838d619860912b1ce39b7727a0709ce0df307", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.5.3", "os": "mac", "version": "0.99.1", "date": "2026-10-12T13:03:59.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/3913d3f6d62944b84723115b59a134436d3dbd439755f1dbc91ce95d09bf92c4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.6.1", "os": "mac", "version": "0.99.1", "date": "2026-10-12T13:02:46.000Z", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/42f411d9d69c4000461b757bde07fb12de2a6496978395c7d1f5cf187d8fd1a9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.6.1", "os": "mac", "version": "0.99.1", "date": "2026-10-12T13:05:28.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/9b98610c26e4447023c2fdb56cebce657cc1524e46d9243c523c66ed915fe2d3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.1", "date": "2026-10-12T13:03:13.000Z", "arch": "emscripten", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/115aac7c2ac532870be5f598f7ba5ca1943f884d9d515f0a313615e4e43b00fd", "status": "success", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.7.0", "os": "win", "version": "0.99.1", "date": "2026-10-12T13:06:07.000Z", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/fca3fbfeaf6e8e5e5d3f2623a2b830c11e9bc580dba4fcec8d30fd5fec61b83e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.7.0", "os": "win", "version": "0.99.1", "date": "2026-10-12T13:02:32.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/a39aa23377026311400fba896861c65dee3241f233817d5b2a379ddbedd715bb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.5.3", "os": "win", "version": "0.99.1", "date": "2026-10-12T13:02:19.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/807f528cc5949c1796840f9f4ad16fcbe571a83efa95be930fff584345f0432b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.6.1", "os": "win", "version": "0.99.1", "date": "2026-10-12T13:06:16.000Z", "arch": "aarch64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/0b9497e01fc5dabfd99400e4e92afebc8678ad1ee9da2bad684db09dd2b18b53", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" }, { "r": "4.6.1", "os": "win", "version": "0.99.1", "date": "2026-10-12T13:02:26.000Z", "arch": "x86_64", "commit": "4e5f2707fdd096b760e5bb4ca60938a3c9836d78", "fileid": "https://r2.ropensci.org/9a81e367b073bf7f55e473b36b893222b10937af3b80267f0f3fbb54309b5063", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/cogdisreslab/actions/runs/38252270632" } ] }