{ "_id": "6a17ea04acfb0bcc41da28c8", "Package": "DAMEfinder", "Type": "Package", "Title": "Finds DAMEs - Differential Allelicly MEthylated regions", "Version": "1.25.0", "Authors@R": "c(person(\"Stephany\", \"Orjuela\", role = c(\"aut\", \"cre\"), \nemail = \"sorjuelal@gmail.com\", comment = c(ORCID = \"0000-0002-1508-461X\")),\nperson(\"Dania\", \"Machlab\", role = \"aut\", email = \"dania.machlab@gmail.com\"),\nperson(\"Mark\", \"Robinson\", role = \"aut\", email = \"mark.robinson@imls.uzh.ch\"))", "Description": "'DAMEfinder' offers functionality for taking methtuple or\nbismark outputs to calculate ASM scores and compute DAMEs. It\nalso offers nice visualization of methyl-circle plots.", "License": "MIT + file LICENSE", "LazyData": "FALSE", "RoxygenNote": "7.2.2", "biocViews": "DNAMethylation, DifferentialMethylation, Coverage", "VignetteBuilder": "knitr", "BugReports": "https://github.com/markrobinsonuzh/DAMEfinder/issues", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:51:43 UTC", "RemoteUrl": "https://github.com/bioc/DAMEfinder", "RemoteRef": "HEAD", "RemoteSha": "49423a64ec25393c1ef4338b82c9761d76ca9930", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:33:01 UTC", "User": "root" }, "Author": "Stephany Orjuela [aut, cre] (ORCID:\n),\nDania Machlab [aut],\nMark Robinson [aut]", "Maintainer": "Stephany Orjuela ", "MD5sum": "b20d787353bcf7e80b6745c9ae50338b", "_user": "bioc", "_type": "src", "_file": "DAMEfinder_1.25.0.tar.gz", "_fileid": "140ced2d561c7b8363639f3dff78f3b73c16d2c1d0176df50135cc0e1f67daf0", "_filesize": 4927999, "_sha256": "140ced2d561c7b8363639f3dff78f3b73c16d2c1d0176df50135cc0e1f67daf0", "_created": "2026-05-28T06:33:01.000Z", "_published": "2026-05-28T07:08:52.838Z", "_jobs": [ { "job": 78236745975, "time": 218, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7259265735" }, { "job": 78236746146, "time": 463, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7259325798" }, { "job": 78236746048, "time": 470, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7259327391" }, { "job": 78236746008, "time": 255, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7259724534" }, { "job": 78236745996, "time": 302, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7259735070" }, { "job": 78235895142, "time": 412, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259209573" }, { "job": 78236745994, "time": 229, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259268291" }, { "job": 78236746042, "time": 462, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7259326157" }, { "job": 78236746011, "time": 373, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7259303532" }, { "job": 78236746017, "time": 366, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7259301939" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/DAMEfinder", "_commit": { "id": "49423a64ec25393c1ef4338b82c9761d76ca9930", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380703 }, "_maintainer": { "name": "Stephany Orjuela", "email": "sorjuelal@gmail.com", "login": "sorjuela", "description": "", "uuid": 24370519, "orcid": "0000-0002-1508-461X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "VariantAnnotation", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "bumphunter", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "dnamethylation", "differentialmethylation", "coverage" ], "_stars": 10, "_contributors": [ { "user": "sorjuela", "count": 43, "uuid": 24370519 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "markrobinsonuzh", "count": 7, "uuid": 6471769 }, { "user": "hpages", "count": 3, "uuid": 8810451 }, { "user": "machlabd", "count": 2, "uuid": 13626534 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 472, "source": "https://www.bioconductor.org/packages/stats/bioc/DAMEfinder" }, "_mentions": 1, "_devurl": "https://github.com/markrobinsonuzh/damefinder", "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DAMEfinder.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/markrobinsonuzh/damefinder", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calc_asm", "calc_derivedasm", "dame_track", "dame_track_mean", "extract_bams", "find_dames", "get_tstats", "methyl_circle_plot", "methyl_circle_plotCpG", "methyl_MDS_plot", "read_tuples" ], "_datasets": [ { "name": "extractbams_output", "title": "extract_bams() output.", "object": "extractbams_output", "file": "extractbams_output.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "readtuples_output", "title": "read_tuples() output.", "object": "readtuples_output", "file": "readtuples_output.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "calc_asm", "title": "Calculate ASM Score", "topics": [ "calc_asm" ] }, { "page": "calc_derivedasm", "title": "Calculate SNP-based ASM", "topics": [ "calc_derivedasm" ] }, { "page": "calc_logodds", "title": "Calculate the log odds ratio", "topics": [ "calc_logodds" ] }, { "page": "calc_score", "title": "Calculate score", "topics": [ "calc_score" ] }, { "page": "calc_weight", "title": "Calculate Weight for ASM Score", "topics": [ "calc_weight" ] }, { "page": "dame_track", "title": "Plot score tracks", "topics": [ "dame_track" ] }, { "page": "dame_track_mean", "title": "Plot means per group of score tracks.", "topics": [ "dame_track_mean" ] }, { "page": "DAMEfinder", "title": "DAMEfinder: Method to detect allele-specific methylation (ASM), and differential ASM from Bisulfite sequencing data in R.", "topics": [ "DAMEfinder" ] }, { "page": "extract_bams", "title": "Detect allele-specific methylation from a bam file", "topics": [ "extract_bams" ] }, { "page": "extractbams_output", "title": "extract_bams() output.", "topics": [ "extractbams_output" ] }, { "page": "find_dames", "title": "Find DAMEs", "topics": [ "find_dames" ] }, { "page": "get_tstats", "title": "Get t-Statistics", "topics": [ "get_tstats" ] }, { "page": "methyl_circle_plot", "title": "Draw methylation circle plot", "topics": [ "methyl_circle_plot" ] }, { "page": "methyl_circle_plotCpG", "title": "Draw methylation circle plot without SNP", "topics": [ "methyl_circle_plotCpG" ] }, { "page": "methyl_MDS_plot", "title": "Multidimensional scaling plot of distances between methylation proportions (beta values)", "topics": [ "methyl_MDS_plot" ] }, { "page": "modulus_sqrt", "title": "Get Modulus Square Root", "topics": [ "modulus_sqrt" ] }, { "page": "read_tuples", "title": "Read in list of methtuple files", "topics": [ "read_tuples" ] }, { "page": "readtuples_output", "title": "read_tuples() output.", "topics": [ "readtuples_output" ] } ], "_readme": "https://github.com/bioc/DAMEfinder/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "bumphunter", "cachem", "cigarillo", "cli", "clipr", "codetools", "cowplot", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "digest", "doRNG", "farver", "fastmap", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gtable", "hms", "httr", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "R6", "RColorBrewer", "Rcpp", "RCurl", "readr", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "rngtools", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyselect", "tzdb", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "vroom", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "DAMEfinder_workflow.Rmd", "filename": "DAMEfinder_workflow.html", "title": "DAMEfinder Workflow", "author": "Stephany Orjuela, Dania Machlab, Mark Robinson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "What is allele-specific methylation?", "Overview", "Why SNP-based?", "Why tuple-based?", "Installation", "Get bam files", "SNP-based (aka slow-mode)", "Example Workflow", "Obtain allele-based methylation calls", "Summarize methylation calls across samples", "Find DAMEs", "tuple-based (aka fast-mode)", "Run Methtuple on bam files", "Read methtuple files", "Calculate ASM Score", "Visualization", "DAME tracks", "Methyl-circle plot", "MDS plot", "Session Info", "References" ], "created": "2017-04-13 17:26:34", "modified": "2023-04-04 16:45:39", "commits": 20 } ], "_score": 6, "_indexed": true, "_nocasepkg": "damefinder", "_universes": [ "bioc", "sorjuela", "markrobinsonuzh" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-28T06:37:34.000Z", "distro": "noble", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "08a0b607fd63fe9b855e050042dd2eb61c55f80eadd0719229d13ef9cd4a884c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-28T06:37:56.000Z", "distro": "noble", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "2fccd83d56d429f5117330f7b98bd6b4435a0c3b97756f9f2712c2e6d9b1b5ab", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-28T07:05:25.000Z", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "3e7a47a92b097348db24b7cde25891e8c050c0f2ffd2bf77c6b6857f0675e33f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-28T07:05:38.000Z", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "5b4114496c003e9dc502e4c9fa7a76fe6570d0539373119385d7bef2ac4a5482", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-28T06:37:30.000Z", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "f56f8068ae4a5ace33dc76c87be626fc28c061d7de60a978a63cce65a57a5c32", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-28T06:37:30.000Z", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "2778388d0071f2c89e779d0e28f3c661dc5cb574ef30e4b737d8e26cb3ae43a9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-28T06:36:09.000Z", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "c208b3059176311d7c347e5e5190c727ee1b4992b872c5e5957a4c7f94450d6f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-28T06:35:58.000Z", "commit": "49423a64ec25393c1ef4338b82c9761d76ca9930", "fileid": "aa457fe829e2d332ba56c9db68c671055bb9aef6f0f57221a0d63304bb10dfa2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558581232" } ] }