{ "_id": "6a1f1ef0b401979e7341ffde", "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": "2026-05-16 09:08:45 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": "2025-11-17 21:53:25 UTC", "RemoteUrl": "https://github.com/SAADAT-Abu/GIMP", "RemoteRef": "HEAD", "RemoteSha": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "Author": "Abu Saadat [cre, aut],\nFrancesco Cecere [aut]", "Maintainer": "Abu Saadat ", "MD5sum": "2cbf3bed3c50d6f2ba8a4c492417fd01", "_user": "saadat-abu", "_type": "src", "_file": "GIMP_0.2.0.tar.gz", "_fileid": "b413c4e45ac1c934d6eca28c7688bfae213297726dd9f4b3bd0d36543d675931", "_filesize": 19156859, "_sha256": "b413c4e45ac1c934d6eca28c7688bfae213297726dd9f4b3bd0d36543d675931", "_created": "2026-05-16T09:08:45.000Z", "_published": "2026-06-02T18:20:32.667Z", "_distro": "noble", "_jobs": [ { "job": 79138147133, "time": 1553, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7032354555" }, { "job": 79138147307, "time": 1548, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7032354077" }, { "job": 79138147324, "time": 1383, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7032333230" }, { "job": 79138147289, "time": 1019, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7032297414" }, { "job": 79138146727, "time": 1363, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7032200402" }, { "job": 79138146467, "time": 1259, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7366273121" }, { "job": 79138147536, "time": 1212, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7032318141" }, { "job": 79138147318, "time": 1120, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7032309143" }, { "job": 79138147480, "time": 1382, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7032336440" } ], "_buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/SAADAT-Abu/GIMP", "_commit": { "id": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "author": "SAADAT-Abu ", "committer": "SAADAT-Abu ", "message": "Updated README\n", "time": 1763416405 }, "_maintainer": { "name": "Abu Saadat", "email": "saadatabu1996@gmail.com", "login": "saadat-abu", "linkedin": "in/abu-saadat-8015001a4", "uuid": 103253429 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "shiny", "role": "Imports" }, { "package": "shinydashboard", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "minfi", "role": "Imports" }, { "package": "IlluminaHumanMethylation450kanno.ilmn12.hg19", "role": "Imports" }, { "package": "IlluminaHumanMethylationEPICanno.ilm10b4.hg19", "role": "Imports" }, { "package": "IlluminaHumanMethylationEPICv2anno.20a1.hg38", "role": "Imports" }, { "package": "IlluminaHumanMethylationEPICmanifest", "role": "Imports" }, { "package": "IlluminaHumanMethylation450kmanifest", "role": "Imports" }, { "package": "IlluminaHumanMethylationEPICv2manifest", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "valr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "viridisLite", "role": "Imports" }, { "package": "ggplotify", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "BiocManager", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "GEOquery", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "readxl", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "AnnotationHub", "role": "Suggests" } ], "_owner": "saadat-abu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 2 }, { "week": "2025-26", "n": 4 }, { "week": "2025-29", "n": 13 }, { "week": "2025-30", "n": 2 }, { "week": "2025-31", "n": 4 }, { "week": "2025-35", "n": 20 }, { "week": "2025-36", "n": 6 }, { "week": "2025-37", "n": 1 }, { "week": "2025-42", "n": 1 }, { "week": "2025-43", "n": 1 }, { "week": "2025-47", "n": 1 } ], "_tags": [], "_topics": [ "dnamethylation", "microarray", "preprocessing", "qualitycontrol", "differentialmethylation", "epigenetics", "methylationarray", "bioinformatics", "methylation-arrays", "shiny-app" ], "_stars": 1, "_contributors": [ { "user": "ngsfc", "count": 98, "uuid": 83638770 }, { "user": "saadat-abu", "count": 90, "uuid": 103253429 } ], "_userbio": { "uuid": 103253429, "type": "user", "name": "Abu Saadat", "description": "Bioinformatician specializing in multi-omics data analysis, including methylation arrays, RNA-seq, WES/WGS, and omics\r\ndata integration. " }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GIMP" }, "_devurl": "https://github.com/saadat-abu/gimp", "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GIMP.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "calculate_detection_pvalues", "check_minfi_functions", "create_bedmeth", "create_sample_sheet_template", "diagnose_geo_dataset", "get_geo_phenotype_data", "GIMP_app", "ICRs_heatmap", "iDMPs", "make_cpgs", "make_ICRs", "plot_cpgs_coverage", "plot_line_ICR", "preview_idat_zip", "process_geo_dataset", "process_geo_with_mappings", "read_idat_zip", "validate_geo_dataset" ], "_datasets": [ { "name": "bed450k", "title": "BED 450K probes", "object": "bed450k", "file": "bed450k.rda", "class": [ "data.frame" ], "fields": [ "chrom", "start", "end", "probeID" ], "rows": 485512, "table": true, "tojson": true }, { "name": "bedEPICv1", "title": "BED EPICv1 probes", "object": "bedEPICv1", "file": "bedEPICv1.rda", "class": [ "data.frame" ], "fields": [ "chrom", "start", "end", "probeID" ], "rows": 865859, "table": true, "tojson": true }, { "name": "bedEPICv2", "title": "BED EPICv2 probes", "object": "bedEPICv2", "file": "bedEPICv2.rda", "class": [ "data.frame" ], "fields": [ "chrom", "start", "end", "probeID" ], "rows": 865859, "table": true, "tojson": true }, { "name": "DMRs.hg19", "title": "Imprinted Regions", "object": "DMRs.hg19", "file": "DMRs.hg19.rda", "class": [ "data.frame" ], "fields": [ "chrom", "start", "end", "ICR" ], "rows": 50, "table": true, "tojson": true }, { "name": "DMRs.hg38", "title": "Imprinted Regions", "object": "DMRs.hg38", "file": "DMRs.hg38.rda", "class": [ "data.frame" ], "fields": [ "chrom", "start", "end", "ICR" ], "rows": 50, "table": true, "tojson": true } ], "_help": [ { "page": "bed450k", "title": "BED 450K probes", "topics": [ "bed450k" ] }, { "page": "bedEPICv1", "title": "BED EPICv1 probes", "topics": [ "bedEPICv1" ] }, { "page": "bedEPICv2", "title": "BED EPICv2 probes", "topics": [ "bedEPICv2" ] }, { "page": "calculate_detection_pvalues", "title": "Alternative Detection P-value Calculation", "topics": [ "calculate_detection_pvalues" ] }, { "page": "check_minfi_functions", "title": "Check Available minfi Functions", "topics": [ "check_minfi_functions" ] }, { "page": "create_bedmeth", "title": "Create BED File Data from Methylation Array Annotations", "topics": [ "create_bedmeth" ] }, { "page": "create_sample_sheet_template", "title": "Create Sample Sheet Template", "topics": [ "create_sample_sheet_template" ] }, { "page": "diagnose_geo_dataset", "title": "Diagnose GEO dataset structure", "topics": [ "diagnose_geo_dataset" ] }, { "page": "DMRs.hg19", "title": "Imprinted Regions", "topics": [ "DMRs.hg19" ] }, { "page": "DMRs.hg38", "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": [ "preview_idat_zip" ] }, { "page": "process_geo_dataset", "title": "Download and process GEO methylation dataset", "topics": [ "process_geo_dataset" ] }, { "page": "process_geo_with_mappings", "title": "Process GEO dataset with user-specified group mappings", "topics": [ "process_geo_with_mappings" ] }, { "page": "read_idat_zip", "title": "Read IDAT Files from ZIP Archive This function extracts and processes IDAT files from a ZIP archive containing IDAT files and a sample sheet, returning a beta value matrix ready for GIMP analysis.", "topics": [ "read_idat_zip" ] }, { "page": "validate_geo_dataset", "title": "Check if GEO ID exists and has IDAT data", "topics": [ "validate_geo_dataset" ] } ], "_readme": "https://github.com/SAADAT-Abu/GIMP/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "backports", "base64", "base64enc", "beanplot", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "biocmake", "BiocManager", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "broom", "bslib", "bumphunter", "cachem", "cellranger", "cigarillo", "cli", "clipr", "codetools", "commonmark", "cpp11", "cpp11bigwig", "crayon", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "DelayedMatrixStats", "digest", "dir.expiry", "doParallel", "doRNG", "dplyr", "DT", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "genefilter", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GEOquery", "ggplot2", "ggplotify", "glue", "gridGraphics", "gtable", "h5mread", "HDF5Array", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "IlluminaHumanMethylation450kanno.ilmn12.hg19", "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylationEPICanno.ilm10b4.hg19", "IlluminaHumanMethylationEPICmanifest", "IlluminaHumanMethylationEPICv2anno.20a1.hg38", "IlluminaHumanMethylationEPICv2manifest", "illuminaio", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mime", "minfi", "multtest", "nlme", "nor1mix", "openssl", "otel", "pheatmap", "pillar", "pkgconfig", "plotly", "plyr", "png", "preprocessCore", "prettyunits", "progress", "promises", "purrr", "quadprog", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RCurl", "readr", "readxl", "rematch", "rentrez", "reshape", "reshape2", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "rmarkdown", "rngtools", "Rsamtools", "RSQLite", "rtracklayer", "rvest", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scrime", "selectr", "Seqinfo", "shiny", "shinydashboard", "siggenes", "snow", "sourcetools", "SparseArray", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "utf8", "valr", "vctrs", "viridisLite", "vroom", "withr", "xfun", "XML", "xml2", "xtable", "XVector", "yaml", "yulab.utils" ], "_score": 2.7403626894942437, "_indexed": true, "_nocasepkg": "gimp", "_universes": [ "saadat-abu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-05-16T09:30:00.000Z", "distro": "noble", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "4708916502327181eaa7b948c4a4cf31f5d50ebaf34c6d2f7efcbb0dac126cd8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" }, { "r": "4.6.0", "os": "linux", "version": "0.2.0", "date": "2026-05-16T09:30:04.000Z", "distro": "noble", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "a6af3a8918f340678722e19b82377b7b8a68d8b7751ecd6aee7e21d2efd9074e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-05-16T09:28:06.000Z", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "d25038a39139674d8622ae5beb146ca917d3da66d874f612bc6a3a0e813eb224", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" }, { "r": "4.6.0", "os": "mac", "version": "0.2.0", "date": "2026-05-16T09:23:10.000Z", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "9c27f5f3f6c519431fdd7693f1abff4569ed085181c1f167561c9272f1a88387", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-05-16T09:24:26.000Z", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "e813587be2502c0269af16615c60c841c8a2a53dfb62223f4b8b4174e9dfd6c9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" }, { "r": "4.5.3", "os": "win", "version": "0.2.0", "date": "2026-05-16T09:23:01.000Z", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "7c917b14e4acd20393c64c9cff808678f842042e0e7114195c5a7f512b4d30ed", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" }, { "r": "4.6.0", "os": "win", "version": "0.2.0", "date": "2026-05-16T09:27:04.000Z", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "4ef5b421287265ffe13b67ef1326f0c47a8854e4938947f5f308ec580b0d0287", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-06-02T18:19:43.000Z", "commit": "1c3e55f6954f57dfb132eda012732130edbe7bb6", "fileid": "af73e27004615002ce95092a180b016be70b755956628839e793aead3d8810fa", "status": "success", "buildurl": "https://github.com/r-universe/saadat-abu/actions/runs/25957690869" } ] }