{ "_id": "6a4942f318cdde069385e8f3", "Package": "ADAMgui", "Type": "Package", "Title": "Activity and Diversity Analysis Module Graphical User Interface", "Version": "1.29.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:50:04 UTC", "RemoteUrl": "https://github.com/bioc/ADAMgui", "RemoteRef": "HEAD", "RemoteSha": "5afaeede947f6f195057dd26702d659bf9d193f7", "Packaged": { "Date": "2026-07-04 11:21:49 UTC", "User": "root" }, "Author": "Giordano Bruno Sanches Seco [aut],\nAndré Luiz Molan [ctb],\nAgnes Takeda [ctb],\nJose Rybarczyk Filho [ctb, cre, ths]", "_user": "bioc", "_type": "src", "_file": "ADAMgui_1.29.0.tar.gz", "_fileid": "https://r2.ropensci.org/f570f3e59dc0ead1a9320d6b244083ff425d6362518dbebdf3081ec679ad431c", "_filesize": 1921081, "_sha256": "f570f3e59dc0ead1a9320d6b244083ff425d6362518dbebdf3081ec679ad431c", "_expires": "2026-10-12T17:29:21.000Z", "_created": "2026-07-04T11:21:49.000Z", "_published": "2026-07-04T17:29:23.810Z", "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061", "_status": "success", "_upstream": "https://github.com/bioc/ADAMgui", "_commit": { "id": "5afaeede947f6f195057dd26702d659bf9d193f7", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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": "resolute", "_jobs": [ { "job": 85152295704, "time": 213, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8081253004" }, { "job": 85152295751, "time": 336, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8081266027" }, { "job": 85152295749, "time": 337, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8081266194" }, { "job": 85152295608, "time": 192, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8081250837" }, { "job": 85152295692, "time": 172, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8081248727" }, { "job": 85152295401, "time": 291, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8081230308" }, { "job": 85152295541, "time": 197, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8081251268" }, { "job": 85152295722, "time": 443, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8081277742" }, { "job": 85152295782, "time": 426, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8081275564" }, { "job": 85152295664, "time": 488, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8081282647" } ], "_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": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_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", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/jrybarczyk/adamgui", "_searchresults": 1, "_rbuild": "4.6.1", "_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", "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": true, "_nocasepkg": "adamgui", "_universes": [ "bioc", "jrybarczyk" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-07-04T11:25:31.000Z", "distro": "resolute", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/6ab6bef58f58196490384c4bc7b83b480ac6bcb9d53ec1950cd70f2afe773391", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" }, { "r": "4.6.1", "os": "linux", "version": "1.29.0", "date": "2026-07-04T11:25:26.000Z", "distro": "resolute", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/859d580b76dbe2c067b89763c3c57ce661affad23643b84efab4fc2d53f33424", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-07-04T11:23:58.000Z", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/e288cf5b9283d3a1498d98e24cabeb901f765ffdbd8e273077e155e42289c430", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" }, { "r": "4.6.1", "os": "mac", "version": "1.29.0", "date": "2026-07-04T11:23:43.000Z", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/3bdf96115b58e23e775f6c47c4c31a371cd98a261ea541977ad5a4133c076b50", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-07-04T11:25:38.000Z", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/379284a81ec4440d1ed8479ddbed2ac890be196992a833c97f46ac9b4c184840", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-07-04T11:27:15.000Z", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/f6c2396480a9f49b276744f06377c75256175a6ffd625d626693545fc3bc9a24", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-07-04T11:26:50.000Z", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/321d6100f9e71b8f39bce13380b9df837d115228a19675622e2d4876df72affe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" }, { "r": "4.6.1", "os": "win", "version": "1.29.0", "date": "2026-07-04T11:28:01.000Z", "commit": "5afaeede947f6f195057dd26702d659bf9d193f7", "fileid": "https://r2.ropensci.org/710ccbf64a93f6522bc2d6c8be0c5dec88c255a95a953a42a7d4c7e9e61e59cd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704500061" } ] }