{ "_id": "6a1f2c36b401979e73425b43", "Package": "mosdef", "Title": "MOSt frequently used and useful Differential Expression\nFunctions", "Version": "1.9.0", "Authors@R": "c(\nperson(\ngiven = \"Leon\", family = \"Dammer\", role = c(\"aut\"),\nemail = \"lc.dammer@gmail.com\", comment = c(ORCID = \"0009-0008-4132-7639\")\n),\nperson(\ngiven = \"Federico\", family = \"Marini\", role = c(\"aut\", \"cre\"),\nemail = \"marinif@uni-mainz.de\", comment = c(ORCID = \"0000-0003-3252-7758\")\n)\n)", "Description": "This package provides functionality to run a number of\ntasks in the differential expression analysis workflow. This\nencompasses the most widely used steps, from running various\nenrichment analysis tools with a unified interface to creating\nplots and beautifying table components linking to external\nwebsites and databases. This streamlines the generation of\ncomprehensive analysis reports.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://github.com/imbeimainz/mosdef", "BugReports": "https://github.com/imbeimainz/mosdef/issues", "Config/testthat/edition": "3", "biocViews": "GeneExpression, Software, Transcription, Transcriptomics,\nDifferentialExpression, Visualization, ReportWriting,\nGeneSetEnrichment, GO", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:03:03 UTC", "RemoteUrl": "https://github.com/bioc/mosdef", "RemoteRef": "HEAD", "RemoteSha": "be5ac3c55d564b8fa242236568a29e147a05f3f4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 10:07:43 UTC", "User": "root" }, "Author": "Leon Dammer [aut] (ORCID: ),\nFederico Marini [aut, cre] (ORCID:\n)", "Maintainer": "Federico Marini ", "MD5sum": "1fc24a191177a3d8b89032ad905bddfd", "_user": "bioc", "_type": "src", "_file": "mosdef_1.9.0.tar.gz", "_fileid": "fa0a2845cb90ba707e9bdca7c6a2f8190e2a233276499b95b1db0c29d73b0bb9", "_filesize": 4432655, "_sha256": "fa0a2845cb90ba707e9bdca7c6a2f8190e2a233276499b95b1db0c29d73b0bb9", "_created": "2026-05-15T10:07:43.000Z", "_published": "2026-06-02T19:17:10.172Z", "_jobs": [ { "job": 79151797356, "time": 326, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7014840723" }, { "job": 79151797842, "time": 803, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7014972040" }, { "job": 79151797547, "time": 694, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7014943223" }, { "job": 79151797655, "time": 429, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", 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"be5ac3c55d564b8fa242236568a29e147a05f3f4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381383 }, "_maintainer": { "name": "Federico Marini", "email": "marinif@uni-mainz.de", "login": "federicomarini", "bluesky": "@federicomarini.bsky.social", "linkedin": "in/federico-marini", "orcid": "0000-0003-3252-7758", "twitter": "@FedeBioinfo", "uuid": 7447478 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "DT", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggforce", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { 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"title": "A sample 'DESeqResults' object", "object": "res_de_macrophage", "file": "res_de_macrophage.RData", "class": [ "DESeqResults" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "dot-info_enrichrun", "title": "Printing some info before the enrichment runs", "topics": [ ".info_enrichrun" ] }, { "page": "buttonifier", "title": "Create sets of buttons for gene symbols", "topics": [ "buttonifier" ] }, { "page": "create_link_dbPTM", "title": "Link to dbPTM database", "topics": [ "create_link_dbPTM" ] }, { "page": "create_link_ENSEMBL", "title": "Link to ENSEMBL database", "topics": [ "create_link_ENSEMBL" ] }, { "page": "create_link_genecards", "title": "Link to the GeneCards database", "topics": [ "create_link_GeneCards" ] }, { "page": "create_link_GO", "title": "Link to AMIGO database", "topics": [ "create_link_GO" ] }, { "page": "create_link_GTEX", "title": "Link to the GTEx Portal", "topics": [ "create_link_GTEX" ] }, { "page": "create_link_HPA", "title": "Link to the Human Protein Atlas", "topics": [ "create_link_HPA" ] }, { "page": "create_link_NCBI", "title": "Link to NCBI database", "topics": [ "create_link_NCBI" ] }, { "page": "create_link_pubmed", "title": "Link to Pubmed", "topics": [ "create_link_PubMed" ] }, { "page": "create_link_UniProt", "title": "Link to UniProt database", "topics": [ "create_link_UniProt" ] }, { "page": "de_table_painter", "title": "DE table painter", "topics": [ "de_table_painter" ] }, { "page": "de_volcano", "title": "Generates a volcano plot using ggplot2", "topics": [ "de_volcano" ] }, { "page": "deresult_to_df", "title": "Generate a table from the 'DESeq2' results", "topics": [ "deresult_to_df" ] }, { "page": "gene_plot", "title": "Plot expression values for a gene", "topics": [ "gene_plot" ] }, { "page": "geneinfo_to_html", "title": "Information on a gene", "topics": [ "geneinfo_to_html" ] }, { "page": "get_annotation_orgdb", "title": "Get an annotation data frame from org db packages", "topics": [ 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