{ "_id": "6a17df4cacfb0bcc41d9d523", "Package": "DEWSeq", "Type": "Package", "Title": "Differential Expressed Windows Based on Negative Binomial\nDistribution", "Version": "1.27.0", "Authors@R": "c(person(\"Sudeep\",\"Sahadevan\",email= \"sahadeva@embl.de\",role=\"aut\"),\nperson(\"Thomas\",\"Schwarzl\",email=\"schwarzl@embl.de\",role=\"aut\"),\nperson(\"bioinformatics team\",\"Hentze\",email=\"biohentze@embl.de\",role=c(\"aut\",\"cre\")))", "Description": "DEWSeq is a sliding window approach for the analysis of\ndifferentially enriched binding regions eCLIP or iCLIP next\ngeneration sequencing data.", "VignetteBuilder": "knitr", "biocViews": "Sequencing, GeneRegulation, FunctionalGenomics,\nDifferentialExpression", "License": "LGPL (>= 3)", "URL": "https://github.com/EMBL-Hentze-group/DEWSeq/", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.1.2", "BugReports": "https://github.com/EMBL-Hentze-group/DEWSeq/issues", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:51:17 UTC", "RemoteUrl": "https://github.com/bioc/DEWSeq", "RemoteRef": "HEAD", "RemoteSha": "4b6691240ddcf510a6a32238a6757348f3c16c56", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:15:35 UTC", "User": "root" }, "Author": "Sudeep Sahadevan [aut],\nThomas Schwarzl [aut],\nbioinformatics team Hentze [aut, cre]", "Maintainer": "bioinformatics team Hentze ", "MD5sum": "3309426b19acfde3cf7ec89bb5803ea4", "_user": "bioc", "_type": "src", "_file": "DEWSeq_1.27.0.tar.gz", "_fileid": "faeaa4aa8fae122c4fb17ae98ea1afc280444ae175a2283b3c705445059201d6", "_filesize": 3291278, "_sha256": "faeaa4aa8fae122c4fb17ae98ea1afc280444ae175a2283b3c705445059201d6", "_created": "2026-05-28T06:15:35.000Z", "_published": "2026-05-28T06:23:08.855Z", "_jobs": [ { "job": 78234676554, "time": 190, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7259006522" }, { "job": 78234676597, "time": 386, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7259052350" }, { "job": 78234676559, "time": 347, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7259043401" }, { "job": 78234676568, "time": 188, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7259048886" }, { "job": 78234676592, "time": 181, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7259046652" }, { "job": 78234028573, "time": 333, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7258960702" }, { "job": 78234676525, "time": 155, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7258997841" }, { "job": 78234676557, "time": 271, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7259025726" }, { "job": 78234676540, "time": 261, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7259023335" }, { "job": 78234676560, "time": 282, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7259028312" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/DEWSeq", "_commit": { "id": "4b6691240ddcf510a6a32238a6757348f3c16c56", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380677 }, "_maintainer": { "name": "bioinformatics team Hentze", "email": "biohentze@embl.de", "login": "hentzelab", "description": "We combine biochemical and systems-level approaches to investigate the connections between gene expression and cell metabolism, and their roles in human disease", "uuid": 55585177 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "R.utils", "role": "Depends" }, { "package": "DESeq2", "role": "Depends" }, { "package": "BiocParallel", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "data.table", "version": ">= 1.11.8", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "IHW", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "generegulation", "functionalgenomics", "differentialexpression", "bioinformatics", "eclip", "ngs-analysis" ], "_stars": 5, "_contributors": [ { "user": "sudeepsahadevan", "count": 164, "uuid": 1842874 }, { "user": "nturaga", "count": 12, "uuid": 2746443 }, { "user": "hentzelab", "count": 6, "uuid": 55585177 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 360, "source": "https://www.bioconductor.org/packages/stats/bioc/DEWSeq" }, "_devurl": "https://github.com/embl-hentze-group/dewseq", "_searchresults": 9, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DEWSeq.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/embl-hentze-group/dewseq", "_realowner": "bioc", "_cranurl": false, "_exports": [ "DESeqDataSetFromSlidingWindows", "extractRegions", "filterCounts", "resultsDEWSeq", "toBED", "topWindowStats" ], "_datasets": [ { "name": "SLBP_K562_w50s20", "title": "ENCODE eCLIP data for SLBP in K562, low count filtered", "object": "SLBP_K562_w50s20", "file": "SLBP_K562_w50s20.rda", "class": [ "DESeqDataSet" ], "fields": [], "table": false, "tojson": false }, { "name": "slbpDds", "title": "ENCODE eCLIP data SLBP in K562", "object": "slbpDds", "file": "slbpDds.rda", "class": [ "DESeqDataSet" ], "fields": [], "table": false, "tojson": false }, { "name": "slbpRegions", "title": "ENCODE eCLIP data SLBP in K562", "object": "slbpRegions", "file": "slbpRegions.rda", "class": [ "data.frame" ], "fields": [ "chromosome", "region_begin", "region_end", "strand", "windows_in_region", "region_length", "padj_min", "padj_mean", "padj_max", "log2FoldChange_min", "log2FoldChange_mean", "log2FoldChange_max", "regionStartId", "gene_id", "gene_name", "gene_type", "gene_region", "Nr_of_region", "Total_nr_of_region", "window_number", "unique_ids" ], "rows": 110, "table": true, "tojson": true }, { "name": "slbpVst", "title": "ENCODE eCLIP data SLBP in K562", "object": "slbpVst", "file": "slbpVst.rda", "class": [ "matrix", "array" ], "fields": [ "IP1", "IP2", "SMI" ], "rows": 28569, "table": true, "tojson": true }, { "name": "slbpWindows", "title": "ENCODE eCLIP data SLBP in K562", "object": "slbpWindows", "file": "slbpWindows.rda", "class": [ "data.frame" ], "fields": [ "chromosome", "begin", "end", "width", "strand", "unique_id", "gene_id", "gene_name", "gene_type", "gene_region", "Nr_of_region", "Total_nr_of_region", "window_number", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "pSlidingWindows", "pSlidingWindows.adj" ], "rows": 8841, "table": true, "tojson": true } ], "_help": [ { "page": "DESeqDataSetFromSlidingWindows", "title": "create DESeq data object", "topics": [ "DESeqDataSetFromSlidingWindows" ] }, { "page": "extractRegions", "title": "extract significant regions", "topics": [ "extractRegions" ] }, { "page": "filterCounts", "title": "filter count data", "topics": [ "filterCounts" ] }, { "page": "resultsDEWSeq", "title": "extract DEWseq results", "topics": [ "resultsDEWSeq" ] }, { "page": "SLBP_K562_w50s20", "title": "ENCODE eCLIP data for SLBP in K562, low count filtered", "topics": [ "SLBP_K562_w50s20" ] }, { "page": "slbpDds", "title": "ENCODE eCLIP data SLBP in K562", "topics": [ "slbpDds" ] }, { "page": "slbpRegions", "title": "ENCODE eCLIP data SLBP in K562", "topics": [ "slbpRegions" ] }, { "page": "slbpVst", "title": "ENCODE eCLIP data SLBP in K562", "topics": [ "slbpVst" ] }, { "page": "slbpWindows", "title": "ENCODE eCLIP data SLBP in K562", "topics": [ "slbpWindows" ] }, { "page": "toBED", "title": "windows/regions to BED", "topics": [ "toBED" ] }, { "page": "topWindowStats", "title": "stats for the top windows in each region", "topics": [ "topWindowStats" ] } ], "_readme": "https://github.com/bioc/DEWSeq/raw/HEAD/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "cli", "codetools", "cpp11", "data.table", "DelayedArray", "DESeq2", "farver", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lambda.r", "lattice", "lifecycle", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "DEWSeq.Rmd", "filename": "DEWSeq.html", "title": "Analyzing eCLIP and iCLIP data with DEWSeq", "author": "Sudeep Sahadevan, Thomas Schwarzl", "engine": "knitr::rmarkdown", "headings": [ "Preface", "Related packages", "Acknowledgements", "Introduction", "Introduction to eCLIP sequencing", "The idea behind DEWSeq", "Understanding the signal", "Binding modes", "Chance of crosslinking", "Background and antibodies", "Enrichment of targets", "Contaminants vs background", "RNA fragment length and RNase concentrations", "Read-throughs", "Early truncations", "Method", "Differentially expressed sliding windows", "Combining significant windows", "Prerequisits for DEWSeq", "Input controls", "Replicates", "Data pre-processing", "Raw data pre-processing", "Crosslink site extraction and counting", "Detection of enriched regions with DEWSeq", "Installation", "Load the library", "Importing data for DEWSeq", "Read data", "Estimating Size Factors", "Prefiltering", "DESeq2 approach", "max window count approach", "Estimate size factors based on a specific set of RNAs", "Estimate size factor for assymetric data", "Differential expressed windows analysis", "Estimate dispersion", "Call differentially bingind regions using wald test", "Significance testing", "Combining regions", "Discussion", "Session Info", "References" ], "created": "2019-09-04 18:48:58", "modified": "2023-10-17 06:29:15", "commits": 51 } ], "_score": 5.477121254719663, "_indexed": true, "_nocasepkg": "dewseq", "_universes": [ "bioc", "hentzelab", "embl-hentze-group" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-05-28T06:19:34.000Z", "distro": "noble", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "ac86d4a0001670b80ac536e197a38f6b42a169c691819ce7338196faef6d074a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" }, { "r": "4.6.0", "os": "linux", "version": "1.27.0", "date": "2026-05-28T06:19:05.000Z", "distro": "noble", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "e3c521763e0ee19a5e8dfaecf7f44631300f9dd5a086acd99d237f0f2c1c4c96", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-05-28T06:20:42.000Z", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "551c2673bb83703e25ccbeafdbe46d82f314f79df9751e18596b5916a522953f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" }, { "r": "4.6.0", "os": "mac", "version": "1.27.0", "date": "2026-05-28T06:20:33.000Z", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "68b126fb8f9278c1a5284d5368baf69c37c3c0c076479e6c68069f03a75df178", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-05-28T06:18:48.000Z", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "b57978a3a77fb9ffe76a6062de9255b8e317666301224bbab543a25e01a75b2a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-05-28T06:17:41.000Z", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "331c1e3ed0f01dd62354d364178dcb688aafbb83517dd03beb834e265a2cea29", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-05-28T06:17:27.000Z", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "63635c6023f3c1ee9122a3c90d63f59565a8637a7b18b0196f0457f7aaa3f1f6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" }, { "r": "4.6.0", "os": "win", "version": "1.27.0", "date": "2026-05-28T06:17:38.000Z", "commit": "4b6691240ddcf510a6a32238a6757348f3c16c56", "fileid": "a72b1c5928f20adba0593200d0027c1589b3150c318b823705b15c0e2a8e2955", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558006169" } ] }