{ "_id": "6a1e8c121d7bb097a0a694fe", "Package": "DGEobj", "Type": "Package", "Title": "Differential Gene Expression (DGE) Analysis Results Data Object", "Version": "1.1.2", "Description": "Provides a flexible container to manage and annotate\nDifferential Gene Expression (DGE) analysis results (Smythe et.\nal (2015) ). The DGEobj has data slots\nfor row (gene), col (samples), assays (matrix n-rows by\nm-samples dimensions) and metadata (not keyed to row, col, or\nassays). A set of accessory functions to deposit, query and\nretrieve subsets of a data workflow has been provided.\nAttributes are used to capture metadata such as species and\ngene model, including reproducibility information such that a\n3rd party can access a DGEobj history to see how each data\nobject was created or modified. Since the DGEobj is\ncustomizable and extensible it is not limited to RNA-seq\nanalysis types of workflows -- it can accommodate nearly any\ndata analysis workflow that starts from a matrix of assays\n(rows) by samples (columns).", "Authors@R": "c(person(\"John\", \"Thompson\", role = \"aut\", email = \"jrt@thompsonclan.org\"),\nperson(\"Connie\", \"Brett\", role = c(\"aut\", \"cre\"), email = \"connie@aggregate-genius.com\"),\nperson(\"Isaac\", \"Neuhaus\", role = \"aut\", email = \"isaac.neuhaus@bms.com\"),\nperson(\"Ryan\", \"Thompson\", role = \"aut\", email = \"rct@thompsonclan.org\"))", "License": "GPL-3", "Language": "en-US", "Encoding": "UTF-8", "biocViews": "", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://cb4ds.r-universe.dev", "Date/Publication": "2025-01-29 21:49:15 UTC", "RemoteUrl": "https://github.com/cb4ds/dgeobj", "RemoteRef": "HEAD", "RemoteSha": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 07:50:38 UTC", "User": "root" }, "Author": "John Thompson [aut],\nConnie Brett [aut, cre],\nIsaac Neuhaus [aut],\nRyan Thompson [aut]", "Maintainer": "Connie Brett ", "MD5sum": "5a75e4a5263d44f98cab3b82a3a4a6ce", "_user": "cb4ds", "_type": "src", "_file": "DGEobj_1.1.2.tar.gz", "_fileid": "6ed7e572b2ee9340d649ade5fc4d1ee8c90dc209ae09bca42421de1803470cf9", "_filesize": 2310265, "_sha256": "6ed7e572b2ee9340d649ade5fc4d1ee8c90dc209ae09bca42421de1803470cf9", "_created": "2026-06-02T07:50:38.000Z", "_published": "2026-06-02T07:53:54.309Z", "_distro": "noble", "_jobs": [ { "job": 79024168896, "time": 146, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7351985077" }, { "job": 79024168825, "time": 156, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7351987769" }, { "job": 79024168979, "time": 153, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": 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"committer": "GitHub ", "message": "Update README.md to https for the CRAN status badge", "time": 1738187355 }, "_maintainer": { "name": "Connie Brett", "email": "connie@aggregate-genius.com", "login": "cb4ds", "description": "Feel free to check out my living resume and connect with me at: https://www.linkedin.com/in/conniebprofile", "uuid": 9085025 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "assertthat", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "conflicted", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "glue", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": 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"https://github.com/cb4ds/dgeobj", "_realowner": "cb4ds", "_cranurl": true, "_releases": [ { "version": "1.0.1", "date": "2020-12-07" }, { "version": "1.0.3", "date": "2021-04-09" }, { "version": "1.1.0", "date": "2022-03-25" }, { "version": "1.1.1", "date": "2022-05-10" }, { "version": "1.1.2", "date": "2022-05-16" } ], "_exports": [ "addItem", "addItems", "annotateDGEobj", "baseType", "baseTypes", "getAttributes", "getBaseType", "getItem", "getItems", "getType", "initDGEobj", "initDGEobjDef", "inventory", "newType", "resetDGEobj", "rmItem", "setAttributes", "showAttributes", "showMeta", "showTypes" ], "_help": [ { "page": "DGEobj-package", "title": "DGEobj Package Overview", "topics": [ "DGEobj-package" ] }, { "page": "sub-.DGEobj", "title": "Subset with square brackets", "topics": [ "[.DGEobj" ] }, { "page": "addItem", "title": "Add a data item", "topics": [ "addItem" ] }, { "page": "addItems", "title": "Add multiple data items", "topics": [ "addItems" ] }, { "page": "annotateDGEobj", "title": "Add annotations", "topics": [ "annotateDGEobj" ] }, { "page": "as.list.DGEobj", "title": "Cast as a simple list", "topics": [ "as.list.DGEobj" ] }, { "page": "baseType", "title": "Get the baseType of an internal data item", "topics": [ "baseType" ] }, { "page": "baseTypes", "title": "Get a list of the available baseTypes", "topics": [ "baseTypes" ] }, { "page": "dim.DGEobj", "title": "Get the \"assay\" dimensions (row/genes by col/samples)", "topics": [ "dim.DGEobj" ] }, { "page": "dimnames.DGEobj", "title": "Get the \"assay\" names (row/genes by col/samples)", "topics": [ "dimnames.DGEobj" ] }, { "page": "getAttributes", "title": "Get all attributes", "topics": [ "getAttributes" ] }, { "page": "getBaseType", "title": "Retrieve data items by baseType", "topics": [ "getBaseType" ] }, { "page": "getItem", "title": "Retrieve a data item by name", "topics": [ "getItem" ] }, { "page": "getItems", "title": "Retrieve multiple data items by name", "topics": [ "getItems" ] }, { "page": "getType", "title": "Retrieve data items by type", "topics": [ "getType" ] }, { "page": "initDGEobj", "title": "Initialize with base data (primaryAssayData, row annotations, col annotations)", "topics": [ "initDGEobj" ] }, { "page": "initDGEobjDef", "title": "Instantiate a class DGEobjDef object.", "topics": [ "initDGEobjDef" ] }, { "page": "inventory", "title": "Retrieve the object inventory", "topics": [ "inventory" ] }, { "page": "newType", "title": "Add a new type definition to a DGEobj", "topics": [ "newType" ] }, { "page": "print.DGEobj", "title": "Print the Inventory", "topics": [ "print.DGEobj" ] }, { "page": "resetDGEobj", "title": "Reset to original data", "topics": [ "resetDGEobj" ] }, { "page": "rmItem", "title": "Removes a named data item", "topics": [ "rmItem" ] }, { "page": "setAttributes", "title": "Set attributes", "topics": [ "setAttributes" ] }, { "page": "showAttributes", "title": "Print attributes", "topics": [ "showAttributes" ] }, { "page": "showMeta", "title": "Retrieve the Key/Value metadata attributes that have a character value and length of 1", "topics": [ "showMeta" ] }, { "page": "showTypes", "title": "Returns and prints the list of all defined types", "topics": [ "showTypes" ] }, { "page": "subset.DGEobj", "title": "Subset internal row or column data", "topics": [ "subset.DGEobj" ] } ], "_readme": "https://github.com/cb4ds/dgeobj/raw/HEAD/README.md", "_rundeps": [ "assertthat", "cli", "glue", "lifecycle", "magrittr", "rlang", "stringi", "stringr", "vctrs" ], "_vignettes": [ { "source": "DGEobj_Overview.Rmd", "filename": "DGEobj_Overview.html", "title": "DGEobj: An S3 Object to Capture and Annotate DGE Workflows", "author": "John R. Thompson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "DGEobj Overview", "DGEobj Nomenclature: Items, Types and Base Types", "DGEobj Structure", "Preserving the Original Data", "Building a DGE data object", "Demonstration Dataset: Rat Liver Slice Compound Treatments", "Initializing a DGEobj from dataframes", "Retrieve GEO data for GSE120804", "Prepare the Design Table", "Retrieve Gene Annotation from Ensembl", "Validate Dataframe Relationships", "Instantiate the DGEobj", "Some basic metadata about the project", "additional descriptive attributes", "Institutional attributes", "Examining a DGE object", "Inventory function", "Examine DGEobj Metadata", "DGEobj Length and Dimensions", "Rownames and Colnames", "Subsetting a DGEobj", "Inventory of a DGEobj", "Adding Items to a DGEobj", "Alignment QC Example", "A Workflow Example", "Automating funArgs Entries", "Batch addition of multiple items", "Pre-defined Item Types", "Adding a New Data Type", "Accessing data in a DGEobj", "Retrieve a single item", "Retrieve multiple items", "Ancillary Functions", "Function baseType", "Querying Metadata Stored in Attributes", "Function rmItem", "Function setAttributes", "Function showMeta", "Technical Information", "Project Meta Data", "Workflow attributes", "Customizing the DGEobj Definition for New Data Types" ], "created": "2019-06-10 14:15:41", "modified": "2022-05-21 20:00:32", "commits": 6 } ], "_score": 5.597695185925513, "_indexed": true, "_nocasepkg": "dgeobj", "_universes": [ "cb4ds" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.2", "date": "2026-06-02T07:53:00.000Z", "distro": "noble", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "c01eacfd75c5fe674ab8f0c1fdd6c1ba2d1a809b8f922a3c48a892b69b1b19f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" }, { "r": "4.6.0", "os": "linux", "version": "1.1.2", "date": "2026-06-02T07:53:07.000Z", "distro": "noble", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "f347259f5ec44f20ab4dbe3a4aa56e7b6f13b5899a7bffaa3b826716ef285a13", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" }, { "r": "4.5.3", "os": "mac", "version": "1.1.2", "date": "2026-06-02T07:52:40.000Z", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "28aeb711d3b25b9bd6e0ea13ef60c8db519ac4c65ea9053c367d7dd69a98a2e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" }, { "r": "4.6.0", "os": "mac", "version": "1.1.2", "date": "2026-06-02T07:52:31.000Z", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "edd4f0e51207ba51226cbf0bc891c4f37a52b3d57d9e5c201a6736ed5f5a530d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.2", "date": "2026-06-02T07:52:52.000Z", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "ad27d4b9bc7ddb338a73a7083794678609c5bc955c3981c2e08f0d66413a686e", "status": "success", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" }, { "r": "4.7.0", "os": "win", "version": "1.1.2", "date": "2026-06-02T07:52:05.000Z", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "e8a846815243bc9eac67206537eb0f6317634dde93a8ed65b305a448d2eb0dc1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" }, { "r": "4.5.3", "os": "win", "version": "1.1.2", "date": "2026-06-02T07:51:58.000Z", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "60161f4104e201abd23f7f736de6f02e6bb287aa31d09bf9d58d9ace9162a39b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" }, { "r": "4.6.0", "os": "win", "version": "1.1.2", "date": "2026-06-02T07:51:52.000Z", "commit": "f9ea01bfe87c2e16378eeae14d575aaf53166e80", "fileid": "55436b15c3d222fd715b9bab042d74131b517557ccd31313ce0d6fd09a9fd1c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cb4ds/actions/runs/26806046868" } ] }