{ "_id": "6a294445732311cd875ab53e", "Package": "Cogito", "Type": "Package", "Title": "Compare genomic intervals tool - Automated, complete,\nreproducible and clear report about genomic and epigenomic data\nsets", "Version": "1.18.0", "Date": "2025-07-28", "Authors@R": "person(\"Annika\", \"Bürger\", email=\"a.buerger@uni-muenster.de\",\nrole=c(\"cre\", \"aut\"))", "Description": "Biological studies often consist of multiple conditions\nwhich are examined with different laboratory set ups like\nRNA-sequencing or ChIP-sequencing. To get an overview about the\nwhole resulting data set, Cogito provides an automated,\ncomplete, reproducible and clear report about all samples and\nbasic comparisons between all different samples. This report\ncan be used as documentation about the data set or as starting\npoint for further custom analysis.", "License": "LGPL-3", "Encoding": "UTF-8", "LazyData": "TRUE", "biocViews": "FunctionalGenomics, GeneRegulation, Software, Sequencing", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Config/pak/sysreqs": "cmake make libbz2-dev liblzma-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:57:13 UTC", "RemoteUrl": "https://github.com/bioc/Cogito", "RemoteRef": "RELEASE_3_23", "RemoteSha": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "Packaged": { "Date": "2026-06-10 10:53:34 UTC", "User": "root" }, "Author": "Annika Bürger [cre, aut]", "Maintainer": "Annika Bürger ", "MD5sum": "1accdb283b4b9ac32830424a9bd886a6", "_user": "bioc-release", "_type": "src", "_file": "Cogito_1.18.0.tar.gz", "_fileid": "46e4ab5a0b6f6511204fa4e616c63ee7a151cbe8e5275b358d37388e87041cd0", "_filesize": 777553, "_sha256": "46e4ab5a0b6f6511204fa4e616c63ee7a151cbe8e5275b358d37388e87041cd0", "_created": "2026-06-10T10:53:34.000Z", "_published": "2026-06-10T11:02:29.594Z", "_jobs": [ { "job": 80541198329, "time": 243, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7533703320" }, { "job": 80541198381, "time": 444, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7533773384" }, { "job": 80541198361, "time": 460, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7533778789" }, { "job": 80541198352, "time": 246, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7533704653" }, { "job": 80541198358, "time": 292, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7533720597" }, { "job": 80540276790, "time": 320, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7533617629" }, { "job": 80541198342, "time": 202, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7533688684" }, { "job": 80541198356, "time": 373, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7533747869" }, { "job": 80541198406, "time": 322, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7533730982" }, { "job": 80541198343, "time": 339, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7533736655" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Cogito", "_commit": { "id": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381033 }, "_maintainer": { "name": "Annika Bürger", "email": "a.buerger@uni-muenster.de", "login": "annikabuerger", "description": "", "uuid": 88655772 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "jsonlite", "role": "Depends" }, { "package": "GenomicFeatures", "role": "Depends" }, { "package": "entropy", "role": "Depends" }, { "package": "BiocManager", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "TxDb.Mmusculus.UCSC.mm9.knownGene", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "functionalgenomics", "generegulation", "software", "sequencing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 304, "source": "https://www.bioconductor.org/packages/stats/bioc/Cogito" }, "_mentions": 5, "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/Cogito.html", "extra/contents.json", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggregateRanges", "summarizeRanges" ], "_datasets": [ { "name": "MurEpi.ChIP.small", "title": "Example data set: Murine ChIP-seq data of GEO GSE77004", "object": "MurEpi.ChIP.small", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "MurEpi.RNA.small", "title": "Example data set: Murine RNA-seq RPKM values of GSE77004", "object": "MurEpi.RNA.small", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "MurEpi.RRBS.small", "title": "Example data set: Murine methylation status data set of GSE77004", "object": "MurEpi.RRBS.small", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "aggregateRanges", "title": "Aggregate GRanges with columns of attached values to genes", "topics": [ "aggregateRanges" ] }, { "page": "MurEpi.ChIP.small", "title": "Example data set: Murine ChIP-seq data of GEO GSE77004", "topics": [ "MurEpi.ChIP.small" ] }, { "page": "MurEpi.RNA.small", "title": "Example data set: Murine RNA-seq RPKM values of GSE77004", "topics": [ "MurEpi.RNA.small" ] }, { "page": "MurEpi.RRBS.small", "title": "Example data set: Murine methylation status data set of GSE77004", "topics": [ "MurEpi.RRBS.small" ] }, { "page": "summarizeRanges", "title": "Summarize Aggregated GRanges", "topics": [ "summarizeRanges" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "digest", "entropy", "evaluate", "farver", "fastmap", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "httr", "IRanges", "isoband", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rappdirs", "RColorBrewer", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "tinytex", "TxDb.Mmusculus.UCSC.mm9.knownGene", "vctrs", "viridisLite", "withr", "xfun", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "Cogito.Rmd", "filename": "Cogito.html", "title": "Cogito: Compare annotated genomic intervals tool", "author": "Annika Buerger", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Workflow", "References", "Session Information" ], "created": "2021-08-12 19:57:54", "modified": "2022-07-07 12:01:22", "commits": 3 } ], "_score": 4.301029995663981, "_indexed": false, "_nocasepkg": "cogito", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/Cogito", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.18.0", "date": "2026-06-10T10:58:37.000Z", "distro": "noble", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "b73905054857526985d23b07b0ac7926bf63c56030edd945a761b95a6a241360", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" }, { "r": "4.6.0", "os": "linux", "version": "1.18.0", "date": "2026-06-10T10:58:15.000Z", "distro": "noble", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "ac8778b1b89990e0a5b0d10bb1ce31f1ab00746bc8a5a6de9102f9c9c807e414", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" }, { "r": "4.5.3", "os": "mac", "version": "1.18.0", "date": "2026-06-10T10:56:07.000Z", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "d24cdf43479579dd42347124b5ad7a55170a1e7f2789ad367f11dfc61cb164fb", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" }, { "r": "4.6.0", "os": "mac", "version": "1.18.0", "date": "2026-06-10T10:56:15.000Z", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "3979a5b61c88195d4e199307bb5714bf7c25a4dbb50210f4b8b7e691df206c97", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" }, { "r": "4.6.0", "os": "wasm", "version": "1.18.0", "date": "2026-06-10T10:57:36.000Z", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "68ae1a9fbba6d9aa82eb399f68178d3b4a75b9b9dbcdb7640016267197ec2e94", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" }, { "r": "4.7.0", "os": "win", "version": "1.18.0", "date": "2026-06-10T10:56:14.000Z", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "63005ea5206f3d4da05ba3dfaee959311e9aaec4e0ff2b181ffa00ff4e7b8220", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" }, { "r": "4.5.3", "os": "win", "version": "1.18.0", "date": "2026-06-10T10:56:10.000Z", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "0c4ec473869d1c4b44b7454df8abf1ad1d203ed05e9f0246c85666c380ff0ec8", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" }, { "r": "4.6.0", "os": "win", "version": "1.18.0", "date": "2026-06-10T10:56:21.000Z", "commit": "3c485cfe8292cfa40e63a2715d7285370cf5bdf9", "fileid": "81a165108fd589bf212160faa2f1722242878c8d24b20a0c3d033c6278e54120", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27271028391" } ] }