{ "_id": "6a17e1e6acfb0bcc41d9f5aa", "Package": "derfinder", "Type": "Package", "Title": "Annotation-agnostic differential expression analysis of RNA-seq\ndata at base-pair resolution via the DER Finder approach", "Version": "1.47.0", "Date": "2025-07-21", "Authors@R": "c(person(\"Leonardo\", \"Collado-Torres\", role = c(\"aut\", \"cre\"), email\n= \"lcolladotor@gmail.com\", comment = c(ORCID = \"0000-0003-2140-308X\")),\nperson(c(\"Alyssa\", \"C.\"), \"Frazee\", role = c(\"ctb\"),\nemail = \"alyssa.frazee@gmail.com\"), person(c(\"Andrew\", \"E.\"), \"Jaffe\",\nrole = \"aut\", email = \"andrew.jaffe@libd.org\",\ncomment = c(ORCID = \"0000-0001-6886-1454\")), person(c(\"Jeffrey\", \"T.\"),\n\"Leek\", role = c(\"aut\", \"ths\"), email = \"jtleek@gmail.com\",\ncomment = c(ORCID = \"0000-0002-2873-2671\")))", "VignetteBuilder": "knitr", "Description": "This package provides functions for annotation-agnostic\ndifferential expression analysis of RNA-seq data. Two\nimplementations of the DER Finder approach are included in this\npackage: (1) single base-level F-statistics and (2) DER\nidentification at the expressed regions-level. The DER Finder\napproach can also be used to identify differentially bounded\nChIP-seq peaks.", "License": "Artistic-2.0", "LazyData": "true", "URL": "https://github.com/lcolladotor/derfinder", "BugReports": "https://support.bioconductor.org/t/derfinder/", "biocViews": "DifferentialExpression, Sequencing, RNASeq, ChIPSeq,\nDifferentialPeakCalling, Software, ImmunoOncology, Coverage", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:50 UTC", "RemoteUrl": "https://github.com/bioc/derfinder", "RemoteRef": "HEAD", "RemoteSha": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:22:31 UTC", "User": "root" }, "Author": "Leonardo Collado-Torres [aut, cre] (ORCID:\n),\nAlyssa C. Frazee [ctb],\nAndrew E. Jaffe [aut] (ORCID: ),\nJeffrey T. Leek [aut, ths] (ORCID:\n)", "Maintainer": "Leonardo Collado-Torres ", "MD5sum": "369fb6e8e267a3a55fb22482cf43a25c", "_user": "bioc", "_type": "src", "_file": "derfinder_1.47.0.tar.gz", "_fileid": "501d23083276ccf45ca5f20fad66ca3acce1fc1f94af1a869d9eb87fb9cdcae5", "_filesize": 1721415, "_sha256": "501d23083276ccf45ca5f20fad66ca3acce1fc1f94af1a869d9eb87fb9cdcae5", "_created": "2026-05-28T06:22:31.000Z", "_published": "2026-05-28T06:34:13.985Z", "_jobs": [ { "job": 78235524799, "time": 232, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7259118600" }, { "job": 78235524792, "time": 621, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7259213980" }, { "job": 78235524846, "time": 594, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7259206853" }, { "job": 78235524844, "time": 378, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7259168502" }, { "job": 78235524801, "time": 419, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7259178376" }, { "job": 78234549776, "time": 503, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259064410" }, { "job": 78235524815, "time": 208, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259112912" }, { "job": 78235524847, "time": 507, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7259184789" }, { "job": 78235524837, "time": 510, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7259186214" }, { "job": 78235524863, "time": 524, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7259189411" } ], "_bioccheck": { "error": 0, "warning": 2, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/derfinder", "_commit": { "id": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379990 }, "_maintainer": { "name": "Leonardo Collado-Torres", "email": "lcolladotor@gmail.com", "login": "lcolladotor", "bluesky": "@lcolladotor.bsky.social", "linkedin": "in/lcollado", "twitter": "@lcolladotor", "description": "Find more information about myself at my website where I post my recent publications, talks, blog posts and other updates.", "uuid": 2288213, "orcid": "0000-0003-2140-308X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.25.1", "role": "Imports" }, { "package": "AnnotationDbi", "version": ">= 1.27.9", "role": "Imports" }, { "package": "BiocParallel", "version": ">= 1.15.15", "role": "Imports" }, { "package": "bumphunter", "version": ">= 1.9.2", "role": "Imports" }, { "package": "derfinderHelper", "version": ">= 1.1.0", "role": "Imports" }, { "package": "Seqinfo", "version": ">= 0.99.2", "role": "Imports" }, { "package": "GenomeInfoDb", "version": ">= 1.45.9", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "GenomicFiles", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.61.1", "role": "Imports" }, { "package": "Hmisc", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.3.23", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "qvalue", "version": ">= 1.99.0", "role": "Imports" }, { "package": "Rsamtools", "version": ">= 2.25.1", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.23.19", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "version": ">= 2.5.19", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "derfinderData", "version": ">= 0.99.0", "role": "Suggests" }, { "package": "derfinderPlot", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.6", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "RefManageR", "role": "Suggests" }, { "package": "rmarkdown", "version": ">= 0.3.3", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "TxDb.Hsapiens.UCSC.hg19.knownGene", "role": "Suggests" }, { "package": "covr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 6, "_updates": [ { "week": "2025-30", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23" } ], "_topics": [ "differentialexpression", "sequencing", "rnaseq", "chipseq", "differentialpeakcalling", "software", "immunooncology", "coverage", "annotation-agnostic", "bioconductor", "derfinder" ], "_stars": 44, "_contributors": [ { "user": "lcolladotor", "count": 820, "uuid": 2288213 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "dtenenba", "count": 10, "uuid": 2286826 }, { "user": "hpages", "count": 10, "uuid": 8810451 }, { "user": "andrewejaffe", "count": 3, "uuid": 625768 }, { "user": "mikelove", "count": 2, "uuid": 69203 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "ttriche", "count": 1, "uuid": 4386 }, { "user": "c1au6i0", "count": 1, "uuid": 47305205 }, { "user": "jtleek", "count": 1, "uuid": 1571674 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1064, "source": "https://www.bioconductor.org/packages/stats/bioc/derfinder" }, "_mentions": 6, "_devurl": "https://github.com/lcolladotor/derfinder", "_searchresults": 77, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/derfinder.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/lcolladotor/derfinder", "_realowner": "bioc", "_cranurl": false, "_exports": [ "advancedArg", "analyzeChr", "annotateRegions", "calculatePvalues", "calculateStats", "coerceGR", "collapseFullCoverage", "coverageToExon", "createBw", "createBwSample", "define_cluster", "extendedMapSeqlevels", "filterData", "findRegions", "fullCoverage", "getRegionCoverage", "getTotalMapped", "loadCoverage", "makeGenomicState", "makeModels", "mergeResults", "preprocessCoverage", "railMatrix", "rawFiles", "regionMatrix", "sampleDepth" ], "_datasets": [ { "name": "genomeData", "title": "Genome samples processed data", "object": "genomeData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "genomeDataRaw", "title": "Genome samples processed data", "object": "genomeDataRaw", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "genomeFstats", "title": "F-statistics for the example data", "object": "genomeFstats", "class": [ "Rle" ], "fields": [], "table": false, "tojson": false }, { "name": "genomeInfo", "title": "Genome samples information", "object": "genomeInfo", "class": [ "data.frame" ], "fields": [ "run", "library.layout", "hapmap.id", "gender", "pop" ], "rows": 31, "table": true, "tojson": true }, { "name": "genomeRegions", "title": "Candidate DERs for example data", "object": "genomeRegions", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "genomicState", "title": "Genomic State for Hsapiens.UCSC.hg19.knownGene", "object": "genomicState", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "analyzeChr", "title": "Run the derfinder analysis on a chromosome", "topics": [ "analyzeChr" ] }, { "page": "annotateRegions", "title": "Assign genomic states to regions", "topics": [ "annotateRegions" ] }, { "page": "calculatePvalues", "title": "Calculate p-values and identify regions", "topics": [ "calculatePvalues" ] }, { "page": "calculateStats", "title": "Calculate F-statistics at base pair resolution from a loaded BAM files", "topics": [ "calculateStats" ] }, { "page": "coerceGR", "title": "Coerce the coverage to a GRanges object for a given sample", "topics": [ "coerceGR" ] }, { "page": "collapseFullCoverage", "title": "Collapse full coverage information for efficient quantile computations", "topics": [ "collapseFullCoverage" ] }, { "page": "coverageToExon", "title": "Extract coverage information for exons", "topics": [ "coverageToExon" ] }, { "page": "createBw", "title": "Export coverage to BigWig files", "topics": [ "createBw" ] }, { "page": "createBwSample", "title": "Create a BigWig file with the coverage information for a given sample", "topics": [ "createBwSample" ] }, { "page": "define_cluster", "title": "Define a cluster to use.", "topics": [ "define_cluster" ] }, { "page": "derfinder-deprecated", "title": "Deprecated functions in package 'derfinder'", "topics": [ "advancedArg", "derfinder-deprecated" ] }, { "page": "extendedMapSeqlevels", "title": "Change naming style for a set of sequence names", "topics": [ "extendedMapSeqlevels" ] }, { "page": "filterData", "title": "Filter the positions of interest", "topics": [ "filterData" ] }, { "page": "findRegions", "title": "Find non-zero regions in a Rle", "topics": [ "findRegions" ] }, { "page": "fullCoverage", "title": "Load the unfiltered coverage information from a group of BAM files and a list of chromosomes", "topics": [ "fullCoverage" ] }, { "page": "genomeData", "title": "Genome samples processed data", "topics": [ "genomeData" ] }, { "page": "genomeDataRaw", "title": "Genome samples processed data", "topics": [ "genomeDataRaw" ] }, { "page": "genomeFstats", "title": "F-statistics for the example data", "topics": [ "genomeFstats" ] }, { "page": "genomeInfo", "title": "Genome samples information", "topics": [ "genomeInfo" ] }, { "page": "genomeRegions", "title": "Candidate DERs for example data", "topics": [ "genomeRegions" ] }, { "page": "genomicState", "title": "Genomic State for Hsapiens.UCSC.hg19.knownGene", "topics": [ "genomicState" ] }, { "page": "getRegionCoverage", "title": "Extract coverage information for a set of regions", "topics": [ "getRegionCoverage" ] }, { "page": "getTotalMapped", "title": "Calculate the total number of mapped reads", "topics": [ "getTotalMapped" ] }, { "page": "loadCoverage", "title": "Load the coverage information from a group of BAM files", "topics": [ "loadCoverage" ] }, { "page": "makeGenomicState", "title": "Obtain the genomic state per region from annotation", "topics": [ "makeGenomicState" ] }, { "page": "makeModels", "title": "Build model matrices for differential expression", "topics": [ "makeModels" ] }, { "page": "mergeResults", "title": "Merge results from different chromosomes", "topics": [ "mergeResults" ] }, { "page": "preprocessCoverage", "title": "Transform and split the data", "topics": [ "preprocessCoverage" ] }, { "page": "railMatrix", "title": "Identify regions data by a coverage filter and get a count matrix from BigWig files", "topics": [ "railMatrix" ] }, { "page": "rawFiles", "title": "Construct full paths to a group of raw input files", "topics": [ "rawFiles" ] }, { "page": "regionMatrix", "title": "Identify regions data by a coverage filter and get a count matrix", "topics": [ "regionMatrix" ] }, { "page": "sampleDepth", "title": "Calculate adjustments for library size", "topics": [ "sampleDepth" ] } ], "_readme": "https://github.com/bioc/derfinder/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "bumphunter", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "derfinderHelper", "digest", "doRNG", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicFiles", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "httr", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "pkgconfig", "plyr", "png", "qvalue", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RCurl", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rngtools", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tinytex", "UCSC.utils", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "derfinder-quickstart.Rmd", "filename": "derfinder-quickstart.html", "title": "derfinder quick start guide", "author": "Leonardo Collado-Torres", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Install r Biocpkg('derfinder')", "Required knowledge", "Asking for help", "Citing r Biocpkg('derfinder')", "Quick start to using to r Biocpkg('derfinder')", "Introduction", "Sample DER Finder analysis", "Reproducibility", "Bibliography" ], "created": "2015-12-09 20:33:33", "modified": "2025-07-22 00:10:22", "commits": 27 }, { "source": "derfinder-users-guide.Rmd", "filename": "derfinder-users-guide.html", "title": "derfinder users guide", "author": "Leonardo Collado-Torres", "engine": "knitr::rmarkdown", "headings": [ "Asking for help", "r Biocpkg('derfinder') users guide", "Expressed regions-level", "regionMatrix()", "railMatrix()", "Single base-level F-statistics", "Example data", "Phenotype data", "Load the data", "Filter coverage", "Expressed region-level analysis", "Via regionMatrix()", "Find DERs with r Biocpkg('DESeq2')", "Find DERs with r Biocpkg('limma')", "Via railMatrix()", "Single base-level F-statistics analysis", "Models", "Find candidate DERs", "Explore results", "optionStats", "coveragePrep", "fstats", "regions", "Nearest annotation", "Time spent", "Merge results", "optionsMerge", "fullRegions", "fullAnnotatedRegions", "ChIP-seq differential binding", "Visually explore results", "Interactive HTML reports", "Miscellaneous features", "Feature level analysis", "Compare results visually", "Export coverage to BigWig files", "Advanced arguments", "Non-human data", "Functions that use multiple cores", "Loading data details", "Controlling loading from BAM files", "Unfiltered base-level coverage", "Input files in a different naming style", "Loading data in chunks", "Large number of samples", "Flow charts", "DER analysis flow chart", "analyzeChr() flow chart", "regionMatrix() flow chart", "Base-level F-statistics projects", "File organization", "bash scripts", "derfinder-analysis.R", "derAnalysis.sh", "Expressed regions-level projects", "Summary", "Reproducibility", "Bibliography" ], "created": "2015-11-11 23:39:13", "modified": "2024-12-12 21:13:08", "commits": 27 } ], "_score": 10.19236877643261, "_indexed": true, "_nocasepkg": "derfinder", "_universes": [ "bioc", "lcolladotor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-05-28T06:27:07.000Z", "distro": "noble", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "5e8fc7540a3a6b21b6620878f370dfb83c55687bc4161eb192dc65c59454cb5d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" }, { "r": "4.6.0", "os": "linux", "version": "1.47.0", "date": "2026-05-28T06:27:25.000Z", "distro": "noble", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "39b8f74be9123399746422ab68779223139a19230e13a206a1d02de02e08d3c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-05-28T06:26:14.000Z", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "ee6e92ff2d5b34dc495114d4856d853d8146a250b2c80ede80a1562756ade1b0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" }, { "r": "4.6.0", "os": "mac", "version": "1.47.0", "date": "2026-05-28T06:26:27.000Z", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "62d8c1d16478a29f0d9ad7956502402e8c767e7a60973320869ad2b57aba1e3f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-05-28T06:26:57.000Z", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "2b921a041ee68279c697d864f4ca7d038253bd813c781619dc1eae4aed9dcffd", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-05-28T06:25:46.000Z", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "68831127344803ecbf47fb52bd44bde795cdaa8efb7fc027ed5577bb620d6cf8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-05-28T06:25:48.000Z", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "76ffbbab3f6880d7f4cd98642bcca5b6a9bbfb9354d0afd98516deac27bbc21d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" }, { "r": "4.6.0", "os": "win", "version": "1.47.0", "date": "2026-05-28T06:25:38.000Z", "commit": "ab0f068105dd0105047165dc148b7633a1f6ebbf", "fileid": "9c6d49e965771d19129e6c62a8da375ab7022a7e07130cda2a8c76b453dec997", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558165001" } ] }