{ "_id": "6a1e964f1d7bb097a0a6c459", "Package": "dinoR", "Title": "Differential NOMe-seq analysis", "Version": "1.8.0", "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-release.r-universe.dev", "Date/Publication": "2026-04-28 13:02:40 UTC", "RemoteUrl": "https://github.com/bioc/dinoR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "5e2387531380d0c9eafc18e937074641e2e2be97", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 08:28:50 UTC", "User": "root" }, "Author": "Michaela Schwaiger [aut, cre] (ORCID:\n)", "Maintainer": "Michaela Schwaiger ", "MD5sum": "fb8cc4e29e3fdccd151a2170be0ae84e", "_user": "bioc-release", "_type": "src", "_file": "dinoR_1.8.0.tar.gz", "_fileid": "beea90a1e0082d24630c50c5ea972bf939f1264b9b09de0c8c97368621ccbdba", "_filesize": 4275561, "_sha256": "beea90a1e0082d24630c50c5ea972bf939f1264b9b09de0c8c97368621ccbdba", "_created": "2026-06-02T08:28:50.000Z", "_published": "2026-06-02T08:37:35.453Z", "_jobs": [ { "job": 79030436734, "time": 181, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7352778393" }, { "job": 79030436760, "time": 337, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7352830819" }, { "job": 79030436784, "time": 322, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7352825989" }, { "job": 79030436728, "time": 172, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7352864242" }, { "job": 79030436865, "time": 203, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7352875167" }, { "job": 79029752405, "time": 246, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7352715725" }, { "job": 79030436738, "time": 127, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7352760312" }, { "job": 79030436799, "time": 245, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7352800549" }, { "job": 79030436774, "time": 244, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7352799637" }, { "job": 79030436827, "time": 295, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7352820773" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/dinoR", "_commit": { "id": "5e2387531380d0c9eafc18e937074641e2e2be97", "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": 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": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_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": 8, "_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/RELEASE_3_23/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": false, "_nocasepkg": "dinor", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/dinoR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.0", "date": "2026-06-02T08:32:26.000Z", "distro": "noble", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "90af5177246215516bf9d8eb138ec16c47f57439f1e65caf1bdf75d81ddb6407", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" }, { "r": "4.6.0", "os": "linux", "version": "1.8.0", "date": "2026-06-02T08:32:25.000Z", "distro": "noble", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "fd12a0e228927f1f3a094a94f926ac11905923af42e28e2cdb1a86d715cdbba7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0", "date": "2026-06-02T08:35:09.000Z", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "84b904269efe9feb697ca9b7b49079b98f8ab2de3dfcd80397d2f2a0bc594912", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" }, { "r": "4.6.0", "os": "mac", "version": "1.8.0", "date": "2026-06-02T08:35:21.000Z", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "0c8ab2a2bce1f9051b1e9de67bcec6858b1573d72ee835627c68e4cb27c10f9a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" }, { "r": "4.6.0", "os": "wasm", "version": "1.8.0", "date": "2026-06-02T08:31:32.000Z", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "70cd2e380afd16e79895e151d9ec1dc669f4f62bf1e5453569c699dc2a06b6cf", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" }, { "r": "4.7.0", "os": "win", "version": "1.8.0", "date": "2026-06-02T08:30:48.000Z", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "e9db8dd3a977ddb239cf646d23c94586c1f54d19ac409be82f2eaf1bfb5df6a2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" }, { "r": "4.5.3", "os": "win", "version": "1.8.0", "date": "2026-06-02T08:30:34.000Z", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "40027981c2058888f3228b1cc321f8d3147ae1bebcac35a67ff1aec3a812c7ee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" }, { "r": "4.6.0", "os": "win", "version": "1.8.0", "date": "2026-06-02T08:31:19.000Z", "commit": "5e2387531380d0c9eafc18e937074641e2e2be97", "fileid": "9de352aebd85c91aadfd53779965a97d250bd94a03e328d305b87b6d50a97430", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807806665" } ] }