{ "_id": "6ac78cd5de46216d5edd2122", "Package": "GIMP", "Title": "Genomic Imprinting Methylation Patterns", "Version": "0.2.0", "Authors@R": "c(\nperson(given = \"Abu\", family = \"Saadat\", role = c(\"cre\", \"aut\"),\nemail = \"saadatabu1996@gmail.com\"),\nperson(given = \"Francesco\", family = \"Cecere\", role = \"aut\",\nemail = \"francesco.cecerengs@gmail.com\"))", "Description": "A package for analyzing Imprinting Control Regions (ICRs)\nDNA methylation. Supports both processed methylation data and\nraw IDAT files from Illumina arrays. Provides specialized tools\nfor imprinting analysis including defect detection and\ninteractive visualizations.", "License": "GPL-3", "Encoding": "UTF-8", "URL": "https://github.com/SAADAT-Abu/GIMP", "BugReports": "https://github.com/SAADAT-Abu/GIMP/issues", "LazyData": "false", "LazyDataCompression": "xz", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "biocViews": "DNAMethylation, Microarray, Preprocessing, QualityControl,\nDifferentialMethylation, Epigenetics, MethylationArray", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 11:27:32 UTC", "User": "root" }, "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev\nxz-utils zlib1g-dev", "Repository": "https://saadat-abu.r-universe.dev", "Date/Publication": "2026-09-08 19:02:35 UTC", "RemoteUrl": "https://github.com/SAADAT-Abu/GIMP", "RemoteRef": "HEAD", "RemoteSha": "b3c382574a5b27503bfa138a2033eb511ab9d903", "Author": "Abu Saadat [cre, aut],\nFrancesco Cecere [aut]", "Maintainer": "Abu Saadat ", "_user": "saadat-abu", "_type": "src", "_file": "GIMP_0.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/27aae64586799b9eaf761a276e53e93b858972b8cdf9b7a3f0d7d7d752d7c40e", "_filesize": 19164369, "_sha256": "27aae64586799b9eaf761a276e53e93b858972b8cdf9b7a3f0d7d7d752d7c40e", "_expires": "2027-01-16T12:30:11.000Z", "_created": "2026-10-08T11:27:32.000Z", "_published": "2026-10-08T12:30:13.723Z", "_buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/37767993392", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113288063146, "time": 1530, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11548668551" }, { "job": 113288063036, "time": 1343, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11547914559" }, { "job": 113288063121, "time": 1433, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11549603998" }, { "job": 113288063081, "time": 1751, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11549444996" }, { "job": 113280384487, "time": 1261, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11547274576" }, { "job": 113288063007, "time": 1233, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11548682722" }, { "job": 113288063321, "time": 1317, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11548124111" }, { "job": 113288063179, "time": 1331, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11547713793" }, { "job": 113288063075, "time": 1160, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11547863983" } ], "_upstream": "https://github.com/SAADAT-Abu/GIMP", "_commit": { "id": "b3c382574a5b27503bfa138a2033eb511ab9d903", "author": "SAADAT-Abu ", "committer": "SAADAT-Abu ", "message": "Add contrast-column selection and plot download to Shiny app\n\n- Replace the old \"Sample_Group\"-named-column auto-shortcut and the\n manual per-sample-only fallback with a unified flow: pick any sample\n sheet column as the contrast, then map each unique value to\n Case/Control/Exclude (mirrors the existing GEO tab's group-mapping\n UX). Opens as a popup right after IDAT processing finishes, with an\n \"Edit Contrast Selection\" button to reopen it if dismissed.\n- Add a download button to the ICR Region Explorer plot, exporting a\n PNG via ggplot2::ggsave() regardless of whether the on-screen plot\n is interactive or static.\n\nVerified via headless-browser-driven testing against real EPICv2 IDAT\ndata (upload, column/mapping selection, DMP analysis, region plot).\n", "time": 1788894155 }, "_maintainer": { "name": "Abu Saadat", "email": "saadatabu1996@gmail.com", "login": "saadat-abu", "linkedin": "in/abu-saadat-8015001a4", "description": "Bioinformatician specializing in multi-omics data analysis, including methylation arrays, RNA-seq, WES/WGS, and omics\ndata integration. 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"title": "Imprinted Regions", "topics": [ "DMRs.hg38" ] }, { "page": "get_geo_phenotype_data", "title": "Get phenotypic data preview for GEO dataset", "topics": [ "get_geo_phenotype_data" ] }, { "page": "GIMP_app", "title": "Launch GIMP Shiny Application", "topics": [ "GIMP_app" ] }, { "page": "ICRs_heatmap", "title": "Generate Heatmap of ICRs Methylation", "topics": [ "ICRs_heatmap" ] }, { "page": "iDMPs", "title": "Identify Differentially Methylated Positions in ICRs", "topics": [ "iDMPs" ] }, { "page": "make_cpgs", "title": "Create ICR CpG Matrix", "topics": [ "make_cpgs" ] }, { "page": "make_ICRs", "title": "Create the ICR Matrix", "topics": [ "make_ICRs" ] }, { "page": "plot_cpgs_coverage", "title": "Plot ICR CpG Matrix with Counts and Percentage Coverage", "topics": [ "plot_cpgs_coverage" ] }, { "page": "plot_line_ICR", "title": "Plot Line Plot for ICR Methylation", "topics": [ "plot_line_ICR" ] }, { "page": "preview_idat_zip", "title": "Preview IDAT ZIP Contents", "topics": [ 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