{ "_id": "6a194e59acfb0bcc41dde81b", "Package": "PANR", "Type": "Package", "Title": "Posterior association networks and functional modules inferred\nfrom rich phenotypes of gene perturbations", "Version": "1.58.0", "Date": "2012-06-20", "Author": "Xin Wang ", "Maintainer": "Xin Wang ", "Description": "This package provides S4 classes and methods for inferring\nfunctional gene networks with edges encoding posterior beliefs\nof gene association types and nodes encoding perturbation\neffects.", "License": "Artistic-2.0", "Collate": "classUnions.R assoScore.R panGraphics.R AllGenerics.R\nAllClasses.R BetaMixture-methods.R PAN-methods.R", "LazyLoad": "yes", "biocViews": "ImmunoOncology, NetworkInference, Visualization,\nGraphAndNetwork, Clustering, CellBasedAssays", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:35:46 UTC", "RemoteUrl": "https://github.com/bioc/PANR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:22:00 UTC", "User": "root" }, "MD5sum": "44d5426183766c43f63ad0c9806120be", "_user": "bioc-release", "_type": "src", "_file": "PANR_1.58.0.tar.gz", "_fileid": "74e9f1f919877f0b7e9416ca9484c9de02d8e8473d813ebe8a8fe117444ac1cb", "_filesize": 2234347, "_sha256": "74e9f1f919877f0b7e9416ca9484c9de02d8e8473d813ebe8a8fe117444ac1cb", "_created": "2026-05-29T07:22:00.000Z", "_published": "2026-05-29T08:29:12.978Z", "_jobs": [ { "job": 78456357822, "time": 135, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7285322916" }, { "job": 78456357862, "time": 185, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7285337521" }, { "job": 78456357836, "time": 147, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7285326789" }, { "job": 78456357883, "time": 188, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7286423349" }, { "job": 78456358009, "time": 220, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7286433129" }, { "job": 78455872436, "time": 212, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285282061" }, { "job": 78456357864, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285315614" }, { "job": 78456357880, "time": 620, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7285467940" }, { "job": 78456357870, "time": 389, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7285398525" }, { "job": 78456357931, "time": 464, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7285421237" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 18 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PANR", "_commit": { "id": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "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": 1777379746 }, "_maintainer": { "name": "Xin Wang", "email": "xin_wang@hms.harvard.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.14", "role": "Depends" }, { "package": "igraph", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pvclust", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "RedeR", "role": "Imports" }, { "package": "snow", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "networkinference", "visualization", "graphandnetwork", "clustering", "cellbasedassays" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 430, "source": "https://www.bioconductor.org/packages/stats/bioc/PANR" }, "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PANR.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "assoScore", "buildPAN", "cosineDist", "cosineSim", "exportPAN", "fitBM", "fitNULL", "infer", "p2SNR", "permNULL", "pvclustModule", "sigModules", "SNR2p", "summarize", "view", "viewLegend", "viewNestedModules", "viewPAN" ], "_datasets": [ { "name": "Bakal2007", "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens", "object": "Bakal2007", "file": "Bakal2007.RData", "class": [ "matrix", "array" ], "fields": [ "CG3799", "RacF28L", "RacV12", "RhoF30L", "RhoV14", "del_RhoGEF3", "del_Sif" ], "rows": 273, "table": true, "tojson": true }, { "name": "Bakal2007Cluster", "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens", "object": "Bakal2007Cluster", "file": "Bakal2007Cluster.RData", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "bm1", "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens", "object": "bm", "file": "bm.RData", "class": [ "BetaMixture" ], "fields": [], "table": false, "tojson": false }, { "name": "nodeColor", "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens", "object": "Bakal2007Cluster", "file": "Bakal2007Cluster.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "assoScore", "title": "Association scores for gene pairs", "topics": [ "assoScore" ] }, { "page": "BetaMixture-class", "title": "An S4 class for beta mixture modelling of functional gene associations", "topics": [ "BetaMixture", "BetaMixture-class" ] }, { "page": "buildPAN", "title": "Build an igraph or RedeR graph for PAN", "topics": [ "buildPAN", "buildPAN,PAN,character_Or_missing,list_Or_missing,logical_Or_missing-method" ] }, { "page": "cosineSim", "title": "Compute cosine similarities or distances between pairs of genes", "topics": [ "cosineDist", "cosineSim" ] }, { "page": "data-Bakal2007", "title": "Rich morphological phenotypes for gene overexpression and RNA interference screens", "topics": [ "Bakal2007", "Bakal2007Cluster", "bm1", "nodeColor" ] }, { "page": "exportPAN", "title": "Export inferred PAN or module graphs to files", "topics": [ "exportPAN", "exportPAN,PAN,character_Or_missing,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method" ] }, { "page": "fitBM", "title": "Fit a three-beta mixture model to densities of functional gene associations", "topics": [ "fitBM", "fitBM,BetaMixture,list_Or_missing,list_Or_missing,logical_Or_missing-method" ] }, { "page": "fitNULL", "title": "Fit the NULL component of a three-beta mixture model for functional gene associations", "topics": [ "fitNULL", "fitNULL,BetaMixture,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing-method" ] }, { "page": "infer", "title": "Infer a posterior association network", "topics": [ "infer", "infer,PAN,list,logical_Or_missing,logical_Or_missing-method" ] }, { "page": "p2SNR", "title": "Translate p-values to Signal-to-Noise Ratios", "topics": [ "p2SNR", "p2SNR,BetaMixture,numeric_Or_integer-method" ] }, { "page": "PAN-class", "title": "An S4 class for inferring a posterior association network", "topics": [ "PAN", "PAN-class" ] }, { "page": "pvclustModule", "title": "Search enriched functional gene modules by pvclust", "topics": [ "pvclustModule", "pvclustModule,PAN,numeric_Or_integer_Or_missing,character_Or_missing,character_Or_missing,logical_Or_missing,logical_Or_missing-method" ] }, { "page": "sigModules", "title": "Retrieve ids for significant gene modules searched by pvclust", "topics": [ "sigModules", "sigModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method" ] }, { "page": "SNR2p", "title": "Translate p-values to Signal-to-Noise Ratios", "topics": [ "SNR2p", "SNR2p,BetaMixture,numeric_Or_integer-method" ] }, { "page": "summarize", "title": "Summarize the object of S4 class 'BetaMixture' or 'PAN'", "topics": [ "summarize", "summarize,BetaMixture,character_Or_missing-method", "summarize,PAN,character_Or_missing-method" ] }, { "page": "view", "title": "View the results of beta-mixture model fitting", "topics": [ "view", "view,BetaMixture,character_Or_missing-method" ] }, { "page": "viewLegend", "title": "View the legends for the graph built for PAN", "topics": [ "viewLegend", "viewLegend,PAN,character_Or_missing-method" ] }, { "page": "viewNestedModules", "title": "View the nested modules in a posterior association network in RedeR", "topics": [ "viewNestedModules", "viewNestedModules,PAN,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,numeric_Or_integer_Or_missing,logical_Or_missing-method" ] }, { "page": "viewPAN", "title": "Show posterior association networks or modules in `igraph' or `RedeR'", "topics": [ "viewPAN", "viewPAN,PAN,character_Or_missing,numeric_Or_integer_Or_missing,character_Or_missing,logical_Or_missing-method" ] } ], "_rundeps": [ "cli", "cpp11", "farver", "glue", "igraph", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "pkgconfig", "pvclust", "R6", "RColorBrewer", "RedeR", "rlang", "scales", "vctrs", "viridisLite" ], "_vignettes": [ { "source": "PANR-Vignette.Rnw", "filename": "PANR-Vignette.pdf", "title": "Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:20:36", "modified": "2013-11-01 20:20:36", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "panr", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/PANR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.58.0", "date": "2026-05-29T07:24:51.000Z", "distro": "noble", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "7048050a92c4237ac19b9b75cba71d0bae362d38d7ceab89221d44077f7711bf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" }, { "r": "4.6.0", "os": "linux", "version": "1.58.0", "date": "2026-05-29T07:24:16.000Z", "distro": "noble", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "fd3bdc1211bacf8fb785290fd79a3a56e89342b60537842dbd7661abad972ab0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" }, { "r": "4.5.3", "os": "mac", "version": "1.58.0", "date": "2026-05-29T08:28:03.000Z", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "7ef9287d494f650e1e5ff52ad8c9915c38fffb406ce3fa3f99d09ae12c40cd50", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" }, { "r": "4.6.0", "os": "mac", "version": "1.58.0", "date": "2026-05-29T08:28:32.000Z", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "f3ca73a61146ff90d4f43a3d18c47a672baca33807dc0dbc3ab4bffdf673b2a8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" }, { "r": "4.6.0", "os": "wasm", "version": "1.58.0", "date": "2026-05-29T07:24:07.000Z", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "dccedef206b9deedca693954cc9799d16e059ff0e2904e5f1309e3401f4798ba", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" }, { "r": "4.7.0", "os": "win", "version": "1.58.0", "date": "2026-05-29T07:31:50.000Z", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "78503874a59f73cbd48b6c1e6e77990f86fc70c12e6abd3dc034eff4a77e92f5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" }, { "r": "4.5.3", "os": "win", "version": "1.58.0", "date": "2026-05-29T07:28:17.000Z", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "250922aefee75eec178e961ffdc27694221c925c6deb290ebe85c047dad90735", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" }, { "r": "4.6.0", "os": "win", "version": "1.58.0", "date": "2026-05-29T07:29:14.000Z", "commit": "f94f21c8a355acd3ea8af5802724f18219b4eb2b", "fileid": "d42a5ab81ef8d63ce41ac662a82a28db802c888d47212c6e5722f59c0d279592", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623865514" } ] }