{ "_id": "6a49440418cdde069385ef06", "Package": "pandaR", "Title": "PANDA Algorithm", "Version": "1.45.0", "Author": "Dan Schlauch, Joseph N. Paulson, Albert Young, John\nQuackenbush, Kimberly Glass", "Maintainer": "Joseph N. Paulson , Dan Schlauch\n", "Description": "Runs PANDA, an algorithm for discovering novel network\nstructure by combining information from multiple complementary\ndata sources.", "biocViews": "StatisticalMethod, GraphAndNetwork, Microarray,\nGeneRegulation, NetworkInference, GeneExpression,\nTranscription, Network", "VignetteBuilder": "knitr", "License": "GPL-2", "LazyData": "true", "RoxygenNote": "6.1.1", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:11 UTC", "RemoteUrl": "https://github.com/bioc/pandaR", "RemoteRef": "HEAD", "RemoteSha": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 14:14:58 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "pandaR_1.45.0.tar.gz", "_fileid": "https://r2.ropensci.org/ea74ac46a56a7e008ff506fbf560f582a288593ce6eec996d29260cd47b5f597", "_filesize": 9356630, "_sha256": "ea74ac46a56a7e008ff506fbf560f582a288593ce6eec996d29260cd47b5f597", "_expires": "2026-10-12T17:33:54.000Z", "_created": "2026-07-04T14:14:58.000Z", "_published": "2026-07-04T17:33:56.181Z", "_bioccheck": { "error": 2, "warning": 4, "note": 16 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174", "_status": "failure", "_upstream": "https://github.com/bioc/pandaR", "_commit": { "id": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380071 }, "_maintainer": { "name": "Joseph N. Paulson", "email": "dschlauch@genospace.com" }, "_distro": "resolute", "_jobs": [ { "job": 85152617477, "time": 202, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8082460105" }, { "job": 85152617343, "time": 224, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "8082462311" }, { "job": 85152617463, "time": 186, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8082458479" }, { "job": 85152617485, "time": 119, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8082450862" }, { "job": 85152617286, "time": 89, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8082447816" }, { "job": 85152617126, "time": 189, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8082437461" }, { "job": 85152617310, "time": 146, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8082453740" }, { "job": 85152617457, "time": 108, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "8082449887" }, { "job": 85152617334, "time": 100, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8082448982" }, { "job": 85152617336, "time": 128, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8082451765" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "BiocGenerics", "role": "Depends" }, { "package": "matrixStats", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "reshape", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "RUnit", "role": "Imports" }, { "package": "hexbin", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "statisticalmethod", "graphandnetwork", "microarray", "generegulation", "networkinference", "geneexpression", "transcription", "network" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 1, "_searchresults": 8, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/contents.json", "extra/pandaR.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calcDegree", "calcDegreeDifference", "importPandaMatlab", "multiplot", "panda", "plotCommunityDetection", "plotGraph", "plotZ", "plotZbyTF", "subnetwork", "summary.panda", "targetedGenes", "testMotif", "topedges" ], "_datasets": [ { "name": "pandaResult", "title": "Analysis result from PANDA algorithm on toy data", "object": "pandaResult", "class": [ "panda" ], "fields": [], "table": false, "tojson": false }, { "name": "pandaResultPairs", "title": "Analysis result from PANDA algorithm on toy data converted into pairs", "object": "pandaResultPairs", "class": [ "data.frame" ], "fields": [ "TF", "Gene", "initial", "Z" ], "rows": 87000, "table": true, "tojson": true }, { "name": "pandaToyData", "title": "Toy gene expression, motif, and ppi data", "object": "pandaToyData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "calcDegree", "title": "Calculate regulatory network degree", "topics": [ "calcDegree" ] }, { "page": "calcDegreeDifference", "title": "Calculate difference in degrees", "topics": [ "calcDegreeDifference" ] }, { "page": "importPandaMatlab", "title": "Panda Matlab importer", "topics": [ "importPandaMatlab" ] }, { "page": "multiplot", "title": "Multiple plots", "topics": [ "multiplot" ] }, { "page": "panda", "title": "Passing Messages between Biological Networks to Refine Predicted Interactions", "topics": [ "panda" ] }, { "page": "pandaR", "title": "pandaR: Passing Messages between Biological Networks to Refine Predicted Interactions.", "topics": [ "pandaR-package", "pandaR" ] }, { "page": "pandaResult", "title": "Analysis result from PANDA algorithm on toy data", "topics": [ "pandaResult" ] }, { "page": "pandaResultPairs", "title": "Analysis result from PANDA algorithm on toy data converted into pairs", "topics": [ "pandaResultPairs" ] }, { "page": "pandaToyData", "title": "Toy gene expression, motif, and ppi data", "topics": [ "pandaToyData" ] }, { "page": "plotCommunityDetection", "title": "Community detection plot", "topics": [ "plotCommunityDetection" ] }, { "page": "plotGraph", "title": "Plot graph", "topics": [ "plotGraph" ] }, { "page": "plotZ", "title": "Comparison of Z scores between two PANDA runs", "topics": [ "plotZ" ] }, { "page": "plotZbyTF", "title": "Plot Z by TF out-degree quantiles", "topics": [ "plotZbyTF" ] }, { "page": "print.panda", "title": "print.panda", "topics": [ "print.panda" ] }, { "page": "subnetwork", "title": "Subnetwork", "topics": [ "subnetwork" ] }, { "page": "summary.panda", "title": "Summary.panda", "topics": [ "summary.panda" ] }, { "page": "targetedGenes", "title": "targetedGenes", "topics": [ "targetedGenes" ] }, { "page": "testMotif", "title": "Check motif", "topics": [ "testMotif" ] }, { "page": "topedges", "title": "Top edges", "topics": [ "topedges" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "cli", "cpp11", "farver", "generics", "ggplot2", "glue", "gtable", "hexbin", "igraph", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "pkgconfig", "plyr", "R6", "RColorBrewer", "Rcpp", "reshape", "rlang", "RUnit", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "pandaR.Rmd", "filename": "pandaR.html", "title": "An Introduction to the pandaR Package", "author": "Daniel Schlauch, Albert Young, Joseph N. Paulson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Example", "Comparing state-specific PANDA networks", "Other helpful functions", "Session information" ], "created": "2015-04-06 22:04:26", "modified": "2016-05-01 20:07:12", "commits": 6 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "pandar", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.0", "date": "2026-07-04T14:18:19.000Z", "distro": "resolute", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/1b09b4e9d2ded1199b8327a4930175f9935b48839244163825d69d1d44da8d53", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" }, { "r": "4.6.1", "os": "linux", "version": "1.45.0", "date": "2026-07-04T14:17:41.000Z", "distro": "resolute", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/71f97b59b091d239d9d066a62e7272cd7c1db42cc2bc202a959e03d3d0d7f58c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" }, { "r": "4.5.3", "os": "mac", "version": "1.45.0", "date": "2026-07-04T14:16:40.000Z", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/43f841c5d4837b6a64502245f2d26ee866ef39c898d8027ad342159c9efc8f47", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" }, { "r": "4.6.1", "os": "mac", "version": "1.45.0", "date": "2026-07-04T14:16:18.000Z", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/a564cbe91e5eab6924ac5203380c0d02e775e9e75ec3133ad20822496ef241ed", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" }, { "r": "4.6.0", "os": "wasm", "version": "1.45.0", "date": "2026-07-04T14:17:41.000Z", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/c653a9e87fe8b4ce95a751379632adb928c29715b2c8898ab6a621338a17001d", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" }, { "r": "4.7.0", "os": "win", "version": "1.45.0", "date": "2026-07-04T14:16:14.000Z", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/53d486e89ef7cff14af92e66cb71dfc4e2f1ec9121be4384e3918d9dc3cf7227", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" }, { "r": "4.5.3", "os": "win", "version": "1.45.0", "date": "2026-07-04T14:16:11.000Z", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/2041f0ceb9049705198792f9bde83463169cc40436587afb5a62cd591a323b0c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" }, { "r": "4.6.1", "os": "win", "version": "1.45.0", "date": "2026-07-04T14:16:32.000Z", "commit": "c5adcb5da7e9803c15e576528f78fa1e1b509a0c", "fileid": "https://r2.ropensci.org/a4342eee441f4e0da5b50360a2ec541ad093cb690c2012a50506c2f3948130bf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28708830174" } ] }