{ "_id": "6a103026acfb0bcc41c954d0", "Package": "dinoR", "Title": "Differential NOMe-seq analysis", "Version": "1.9.0", "Authors@R": "person(\"Michaela\", \"Schwaiger\",, \"michaela.schwaiger@fmi.ch\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4522-7810\"))", "Description": "dinoR tests for significant differences in NOMe-seq\nfootprints between two conditions, using genomic regions of\ninterest (ROI) centered around a landmark, for example a\ntranscription factor (TF) motif. This package takes NOMe-seq\ndata (GCH methylation/protection) in the form of a Ranged\nSummarized Experiment as input. dinoR can be used to group\nsequencing fragments into 3 or 5 categories representing\ncharacteristic footprints (TF bound, nculeosome bound, open\nchromatin), plot the percentage of fragments in each category\nin a heatmap, or averaged across different ROI groups, for\nexample, containing a common TF motif. It is designed to\ncompare footprints between two sample groups, using edgeR's\nquasi-likelihood methods on the total fragment counts per ROI,\nsample, and footprint category.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "LazyData": "false", "biocViews": "NucleosomePositioning, Epigenetics, MethylSeq,\nDifferentialMethylation, Coverage, Transcription, Sequencing,\nSoftware", "URL": "https://github.com/xxxmichixxx/dinoR", "BugReports": "https://github.com/xxxmichixxx/dinoR/issues", "Config/pak/sysreqs": "libicu-dev libpng-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:40 UTC", "RemoteUrl": "https://github.com/bioc/dinoR", "RemoteRef": "HEAD", "RemoteSha": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 09:42:25 UTC", "User": "root" }, "Author": "Michaela Schwaiger [aut, cre] (ORCID:\n)", "Maintainer": "Michaela Schwaiger ", "MD5sum": "5e2197b5203c5efba0383066afb3df6a", "_user": "bioc", "_type": "src", "_file": "dinoR_1.9.0.tar.gz", "_fileid": "8d86eb1435f57950d026b87749c78385917b3bb6ac58d0fcd9225b681b757ed5", "_filesize": 4277235, "_sha256": "8d86eb1435f57950d026b87749c78385917b3bb6ac58d0fcd9225b681b757ed5", "_created": "2026-05-12T09:42:25.000Z", "_published": "2026-05-22T10:29:58.077Z", "_jobs": [ { "job": 77361915220, "time": 197, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "6940849534" }, { "job": 77361915496, "time": 348, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6940901342" }, { "job": 77361915522, "time": 288, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6940879672" }, { "job": 77361915811, "time": 184, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6940931738" }, { "job": 77361915237, "time": 223, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6940943005" }, { "job": 77361914999, "time": 299, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6940782544" }, { "job": 77361914855, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7158371899" }, { "job": 77361915352, "time": 243, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6940864473" }, { "job": 77361915725, "time": 227, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6940859468" }, { "job": 77361915721, "time": 232, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6940860896" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/dinoR", "_commit": { "id": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381360 }, "_maintainer": { "name": "Michaela Schwaiger", "email": "michaela.schwaiger@fmi.ch", "orcid": "0000-0002-4522-7810" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "nucleosomepositioning", "epigenetics", "methylseq", "differentialmethylation", "coverage", "transcription", "sequencing", "software" ], "_stars": 0, "_contributors": [ { "user": "xxxmichixxx", "count": 17, "uuid": 10323206 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 274, "source": "https://www.bioconductor.org/packages/stats/bioc/dinoR" }, "_devurl": "https://github.com/xxxmichixxx/dinor", "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/dinoR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/xxxmichixxx/dinor", "_realowner": "bioc", "_cranurl": false, "_exports": [ "compareFootprints", "createExampleData", "diNOMeTest", "footprintCalc", "footprintPerc", "footprintQuant", "fpPercHeatmap", "metaPlots" ], "_datasets": [ { "name": "NomeData", "title": "NOMeseq data for WT and AdnpKO mouse ES cells", "object": "NomeData", "file": "NomeData.rda", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "compareFootprints", "title": "compareFootprints", "topics": [ "compareFootprints" ] }, { "page": "createExampleData", "title": "createExampleData", "topics": [ "createExampleData" ] }, { "page": "diNOMeTest", "title": "diNOMeTest", "topics": [ "diNOMeTest" ] }, { "page": "footprintCalc", "title": "footprintCalc", "topics": [ "footprintCalc" ] }, { "page": "footprintPerc", "title": "footprintPerc", "topics": [ "footprintPerc" ] }, { "page": "footprintQuant", "title": "footprintQuant", "topics": [ "footprintQuant" ] }, { "page": "fpPercHeatmap", "title": "fpPercHeatmap", "topics": [ "fpPercHeatmap" ] }, { "page": "metaPlots", "title": "metaPlots", "topics": [ "metaPlots" ] }, { "page": "NomeData", "title": "NOMeseq data for WT and AdnpKO mouse ES cells", "topics": [ "NomeData" ] } ], "_readme": "https://github.com/bioc/dinoR/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cowplot", "cpp11", "crayon", "DelayedArray", "digest", "doParallel", "dplyr", "edgeR", "farver", "foreach", "generics", "GenomicRanges", "GetoptLong", "ggplot2", "GlobalOptions", "glue", "gtable", "IRanges", "isoband", "iterators", "labeling", "lattice", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "png", "purrr", "R6", "RColorBrewer", "rjson", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "dinoR-vignette.Rmd", "filename": "dinoR-vignette.html", "title": "dinoR-vignette", "author": "Michaela Schwaiger", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Load the NOMe-seq data for ADNP Knock-Out and", "WT mouse ES cells (two replicates each)", "Meta plots across ROIs with common TF motifs in the center", "Determine fragment counts for five chromatin patterns:", "TF, open, upNuc, downNuc, Nuc", "Calculate differential NOMe-seq footprint abundance between ADNP KO and WT", "Calculate the percentage of fragments in each footprint type and", "plot a (clustered) heatmap comparing percentages in WT and ADNP KO", "Compare the footprint percentages and significance testing", "results for ADNP KO and WT", "Combining the nucleosome patterns", "Session information" ], "created": "2024-01-17 11:51:18", "modified": "2024-03-06 08:32:40", "commits": 4 } ], "_score": 4, "_indexed": true, "_nocasepkg": "dinor", "_universes": [ "bioc", "xxxmichixxx" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-05-12T09:46:04.000Z", "distro": "noble", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "b53661dc702beb4db0d42c45033cc7109d57ef919071e3ef6382d4522f708adf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" }, { "r": "4.6.0", "os": "linux", "version": "1.9.0", "date": "2026-05-12T09:45:34.000Z", "distro": "noble", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "1a39766f969a039f1c24fca0f485a1d0f8a89f3697d4f6bd5eb38605af14bbaa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-05-12T09:48:50.000Z", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "c131762904ed67614b33522a76f18367f84574cf8934c6a6381be0c19accccd4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" }, { "r": "4.6.0", "os": "mac", "version": "1.9.0", "date": "2026-05-12T09:48:52.000Z", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "16e57853a6ecbe6607d809717068efa886b9ed531fc5f8257fb9c6501b633dff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-05-12T09:44:05.000Z", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "35acf5a7acbef8317448b77dd5267e61f17de2fc7b499bf03f51c224956b2129", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-05-12T09:44:02.000Z", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "7c95b20565e5cb9cfadc44a94d3676d0676ab4b49c8f3077cdf868796a3e26bc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" }, { "r": "4.6.0", "os": "win", "version": "1.9.0", "date": "2026-05-12T09:44:02.000Z", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "804226b427c8261d704c8b4c6358985b1aa26ab0ff4e6a45312a7df711d3c766", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-05-22T10:29:34.000Z", "commit": "0fdd65982f6ea095de1494c8fe1de702157a8bc3", "fileid": "9b3bb84c202646b114bcdab82794263fd9c07805950389348923b70a127fa44c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25726220784" } ] }