{ "_id": "6a196c77acfb0bcc41dea91f", "Package": "ADAMgui", "Type": "Package", "Title": "Activity and Diversity Analysis Module Graphical User Interface", "Version": "1.28.0", "Date": "2021-09-01", "Authors@R": "c(person(given = \"Giordano Bruno\",\nfamily = \"Sanches Seco\",\nrole = \"aut\",\nemail = \"giordano.bruno@unesp.br\"),\nperson(given = \"André Luiz\",\nfamily = \"Molan\",\nrole = \"ctb\"),\nperson(given = \"Agnes\",\nfamily = \"Takeda\",\nrole = \"ctb\"),\nperson(given = \"Jose\",\nfamily = \"Rybarczyk Filho\",\nrole = c(\"ctb\", \"cre\", \"ths\"),\nemail = \"jose.luiz@unesp.br\")\n)", "Maintainer": "Jose Luiz Rybarczyk Filho ", "Description": "ADAMgui is a Graphical User Interface for the ADAM\npackage. The ADAMgui package provides 2 shiny-based\napplications that allows the user to study the output of the\nADAM package files through different plots. It's possible, for\nexample, to choose a specific GFAG and observe the gene\nexpression behavior with the plots created with the\nGFAGtargetUi function. Features such as differential expression\nand foldchange can be easily seen with aid of the plots made\nwith GFAGpathUi function.", "biocViews": "GeneSetEnrichment, Pathways, KEGG", "VignetteBuilder": "knitr", "LazyLoad": "yes", "NeedsCompilation": "no", "Encoding": "UTF-8", "RoxygenNote": "6.1.1", "License": "GPL (>= 2)", "URL": "TBA", "BugReports": "https://github.com/jrybarczyk/ADAMgui/issues", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:50:04 UTC", "RemoteUrl": "https://github.com/bioc/ADAMgui", "RemoteRef": "RELEASE_3_23", "RemoteSha": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "Packaged": { "Date": "2026-05-29 08:38:25 UTC", "User": "root" }, "Author": "Giordano Bruno Sanches Seco [aut],\nAndré Luiz Molan [ctb],\nAgnes Takeda [ctb],\nJose Rybarczyk Filho [ctb, cre, ths]", "MD5sum": "7eb33e4bc0cdee7172dda400b49a97ee", "_user": "bioc-release", "_type": "src", "_file": "ADAMgui_1.28.0.tar.gz", "_fileid": "2144b702256909f70aa3e22e3a8f5bbf5e489a78763feaaef59ae506dd535d4c", "_filesize": 1919830, "_sha256": "2144b702256909f70aa3e22e3a8f5bbf5e489a78763feaaef59ae506dd535d4c", "_created": "2026-05-29T08:38:25.000Z", "_published": "2026-05-29T10:37:43.398Z", "_jobs": [ { "job": 78467099469, "time": 218, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7286675787" }, { "job": 78467099479, "time": 369, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7286720333" }, { "job": 78467099497, "time": 386, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7286725471" }, { "job": 78467099490, "time": 218, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7288724827" }, { "job": 78467099535, "time": 218, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7288728856" }, { "job": 78466392856, "time": 290, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286611402" }, { "job": 78467099481, "time": 170, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286660765" }, { "job": 78467099499, "time": 499, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7286758733" }, { "job": 78467099568, "time": 399, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7286729425" }, { "job": 78467099477, "time": 466, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7286749225" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ADAMgui", "_commit": { "id": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "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": 1777380604 }, "_maintainer": { "name": "Jose Luiz Rybarczyk Filho", "email": "jose.luiz@unesp.br", "login": "jrybarczyk", "description": "", "uuid": 13757354 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "ADAM", "role": "Depends" }, { "package": "GO.db", "version": ">= 3.5.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 0.7.6", "role": "Imports" }, { "package": "shiny", "version": ">= 1.1.0", "role": "Imports" }, { "package": "stringr", "version": ">= 1.3.1", "role": "Imports" }, { "package": "stringi", "version": ">= 1.2.4", "role": "Imports" }, { "package": "varhandle", "version": ">= 2.0.3", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.0.0", "role": "Imports" }, { "package": "ggrepel", "version": ">= 0.8.0", "role": "Imports" }, { "package": "ggpubr", "version": ">= 0.1.8", "role": "Imports" }, { "package": "ggsignif", "version": ">= 0.4.0", "role": "Imports" }, { "package": "reshape2", "version": ">= 1.4.3", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 1.1-2", "role": "Imports" }, { "package": "colorRamps", "version": ">= 2.3", "role": "Imports" }, { "package": "DT", "version": ">= 0.4", "role": "Imports" }, { "package": "data.table", "version": ">= 1.11.4", "role": "Imports" }, { "package": "gridExtra", "version": ">= 2.3", "role": "Imports" }, { "package": "shinyjs", "version": ">= 1.0", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "testthat", "role": "Imports" }, { "package": "markdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "genesetenrichment", "pathways", "kegg" ], "_stars": 0, "_contributors": [ { "user": "bads752", "count": 60, "uuid": 31425551 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 444, "source": "https://www.bioconductor.org/packages/stats/bioc/ADAMgui" }, "_devurl": "https://github.com/jrybarczyk/adamgui", "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/ADAMgui.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/jrybarczyk/adamgui", "_realowner": "bioc", "_cranurl": false, "_exports": [ "GFAGpathUi", "GFAGtargetUi" ], "_datasets": [ { "name": "DiffAedes", "title": "Aedes aegypti RNA-seq differential expression data example", "object": "DiffAedes", "file": "DiffAedes.rda", "class": [ "data.frame" ], "fields": [ "gene", "logFC", "q_value" ], "rows": 1973, "table": true, "tojson": true }, { "name": "GeneFunctionAedes", "title": "Relation between Aedes aegypti genes and KEGG pathways", "object": "GeneFunctionAedes", "file": "GeneFunctionAedes.rda", "class": [ "data.frame" ], "fields": [ "gene", "GroupID" ], "rows": 782, "table": true, "tojson": true }, { "name": "ResultAnalysisAedes", "title": "Result from an example of ADAM Aedes aegypti analysis", "object": "ResultAnalysisAedes", "file": "ResultAnalysisAedes.rda", "class": [ "data.frame" ], "fields": [ "ID", "Description", "Raw_Number_Genes", "Sample_Number_Genes", "H_control1", "H_experiment1", "N_control1", "N_experiment1", "h", "n", "pValue_h", "pValue_n", "qValue_h", "qValue_n", "Significance_h", "Significance_n", "Wilcox_pvalue", "Wilcox_qvalue", "Wilcox_significance", "Fisher_pvalue", "Fisher_qvalue", "Fisher_significance" ], "rows": 87, "table": true, "tojson": true } ], "_help": [ { "page": "DiffAedes", "title": "Aedes aegypti RNA-seq differential expression data example", "topics": [ "DiffAedes" ] }, { "page": "GeneFunctionAedes", "title": "Relation between Aedes aegypti genes and KEGG pathways", "topics": [ "GeneFunctionAedes" ] }, { "page": "GFAGpathUi", "title": "GFAGpathUi", "topics": [ "GFAGpathUi" ] }, { "page": "GFAGtargetUi", "title": "GFAGtargetUi", "topics": [ "GFAGtargetUi" ] }, { "page": "ResultAnalysisAedes", "title": "Result from an example of ADAM Aedes aegypti analysis", "topics": [ "ResultAnalysisAedes" ] } ], "_rundeps": [ "abind", "ADAM", "AnnotationDbi", "askpass", "backports", "base64enc", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "boot", "brio", "broom", "bslib", "cachem", "callr", "car", "carData", "cli", "colorRamps", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "Deriv", "desc", "diffobj", "digest", "doBy", "dplyr", "DT", "evaluate", "farver", "fastmap", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "generics", "GenomicRanges", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", "GO.db", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "IRanges", "isoband", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "otel", "pbapply", "pbkrtest", "pillar", "pkgbuild", "pkgconfig", "pkgload", "plyr", "png", "polynom", "praise", "processx", "promises", "ps", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rlang", "rmarkdown", "rprojroot", "RSQLite", "rstatix", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "shiny", "shinyjs", "sourcetools", "SparseArray", "SparseM", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "testthat", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "varhandle", "vctrs", "viridisLite", "waldo", "withr", "xfun", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "ADAMgui.Rmd", "filename": "ADAMgui.html", "title": "ADAMgui: Activity and Diversity Analysis Module Graphical User Interface", "author": "Giordano B. S. Seco, André L. Molan, Agnes A. S. Takeda, Jose L. Rybarczyk-Filho", "engine": "knitr::knitr", "headings": [ "Overview", "Package Download and Installation", "Graphical User Interface (GUI)", "GFAG Path Viewer Function: GFAGpathUi()", "GFAG Target Viewer Function: GFAGtargetUi()", "Session Info", "References" ], "created": "2019-02-06 15:19:57", "modified": "2025-04-11 02:25:33", "commits": 6 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "adamgui", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/ADAMgui", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.28.0", "date": "2026-05-29T08:42:16.000Z", "distro": "noble", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "c61ad1a4d0c513185b1ef79d52c2a28ea9fb9ed8773e32ae0a0dab84bca60c6c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" }, { "r": "4.6.0", "os": "linux", "version": "1.28.0", "date": "2026-05-29T08:42:55.000Z", "distro": "noble", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "6e25d4104a578814fce92f51e11da92a4b8ee928234798ecaa6c9dd98746c76c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" }, { "r": "4.5.3", "os": "mac", "version": "1.28.0", "date": "2026-05-29T10:35:12.000Z", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "20f41a77110cf431aaba78fcd213e31160026753ce4adf1159e79dc112ab509f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" }, { "r": "4.6.0", "os": "mac", "version": "1.28.0", "date": "2026-05-29T10:35:32.000Z", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "9382248b5fa1718c80157ab35cc7f6597963c0627069da761b5d1f93e98cdc58", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" }, { "r": "4.6.0", "os": "wasm", "version": "1.28.0", "date": "2026-05-29T08:41:49.000Z", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "f5fe81f24be1ac7b5bbc0647b68217ffa61f9adf980a11824ef8a23400887ae4", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" }, { "r": "4.7.0", "os": "win", "version": "1.28.0", "date": "2026-05-29T08:44:26.000Z", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "e920dde78871766449e7b0869d74052d23267405949aa14d00f0875393e74bfc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" }, { "r": "4.5.3", "os": "win", "version": "1.28.0", "date": "2026-05-29T08:43:11.000Z", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "e38b8baf95b652c31e05c39224d1c130e2e64be49f70775f3d4c8bd71476fe48", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" }, { "r": "4.6.0", "os": "win", "version": "1.28.0", "date": "2026-05-29T08:44:05.000Z", "commit": "1e3639e8d6e35c7998b84b5ed7505530c3613b7c", "fileid": "f9e3332585813f461cf7b62ebdd6ca42d82525143da2001eec7b84bb02fc0ac4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26627072230" } ] }