{ "_id": "6a33dacd3efcd9bda43b7008", "Package": "RiboDiPA", "Type": "Package", "Title": "Differential pattern analysis for Ribo-seq data", "Date": "2024-03-19", "Version": "1.21.0", "Authors@R": "c(person(given = \"Keren\",\nfamily = \"Li\",\nrole = c(\"aut\"),\nemail = \"keren.li@northwestern.edu\"),\nperson(given = \"Matt\",\nfamily = \"Hope\",\nrole = \"aut\"),\nperson(given = \"Xiaozhong\",\nfamily = \"Wang\",\nrole = \"aut\"),\nperson(given = \"Ji-Ping\",\nfamily = \"Wang\",\nrole = c(\"aut\",\"cre\"),\nemail = \"jzwang@northwestern.edu\"))", "Description": "This package performs differential pattern analysis for\nRibo-seq data. It identifies genes with significantly different\npatterns in the ribosome footprint between two conditions.\nRiboDiPA contains five major components including bam file\nprocessing, P-site mapping, data binning, differential pattern\nanalysis and footprint visualization.", "License": "LGPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "NeedsCompilation": "yes", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "biocViews": "RiboSeq, GeneExpression, GeneRegulation,\nDifferentialExpression, Sequencing, Coverage, Alignment,\nRNASeq, ImmunoOncology, QualityControl, DataImport, Software,\nNormalization", "git_url": "https://git.bioconductor.org/packages/RiboDiPA", "git_branch": "master", "git_last_commit": "7a819c5", "git_last_commit_date": "2021-05-19", "Packaged": { "Date": "2026-06-18 11:26:16 UTC", "User": "root" }, "Author": "Keren Li [aut], Matt Hope [aut], Xiaozhong Wang [aut], Ji-Ping\nWang [aut, cre]", "Maintainer": "Ji-Ping Wang ", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:50 UTC", "RemoteUrl": "https://github.com/bioc/RiboDiPA", "RemoteRef": "HEAD", "RemoteSha": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "MD5sum": "a20f66c75a7de98bdf5400e8f4ebb9ff", "_user": "bioc", "_type": "src", "_file": "RiboDiPA_1.21.0.tar.gz", "_fileid": "b0db179750167547f5ddca8e4a94bf1f697d011f51051ae092043d28a53e28ea", "_filesize": 1845483, "_sha256": "b0db179750167547f5ddca8e4a94bf1f697d011f51051ae092043d28a53e28ea", "_created": "2026-06-18T11:26:16.000Z", "_published": "2026-06-18T11:47:25.689Z", "_jobs": [ { "job": 82118727389, "time": 225, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7722039279" }, { "job": 82118727365, "time": 640, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7722185928" }, { "job": 82118727376, "time": 788, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7722233318" }, { "job": 82118727404, "time": 702, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7722206481" }, { "job": 82118727368, "time": 788, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7722233576" }, { "job": 82118727378, "time": 450, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7722194344" }, { "job": 82118727408, "time": 855, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7722298663" }, { "job": 82118727409, "time": 505, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7722212395" }, { "job": 82118727379, "time": 1058, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7722366392" }, { "job": 82117129859, "time": 561, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7721960169" }, { "job": 82118727356, "time": 200, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7722029736" }, { "job": 82118727377, "time": 709, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7722211525" }, { "job": 82118727412, "time": 721, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7722212215" }, { "job": 82118727386, "time": 755, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7722223068" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RiboDiPA", "_commit": { "id": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380890 }, "_maintainer": { "name": "Ji-Ping Wang", "email": "jzwang@northwestern.edu", "login": "jipingw", "description": "Professor in Statistics and Data Science, Adjunct Professor of Molecular BioSciences. My research interest is in interface of statistics and bi-medical sciences", "uuid": 45120092 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Rsamtools", "role": "Depends" }, { "package": "GenomicFeatures", "role": "Depends" }, { "package": "GenomicAlignments", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.2", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "elitism", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "reldist", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "BiocFileCache", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "txdbmaker", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "riboseq", "geneexpression", "generegulation", "differentialexpression", "sequencing", "coverage", "alignment", "rnaseq", "immunooncology", "qualitycontrol", "dataimport", "software", "normalization", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/RiboDiPA.html", "manual.pdf" ], "_homeurl": "https://github.com/jipingw/ribodipa", "_realowner": "bioc", "_cranurl": false, "_exports": [ "binTrack", "bpTrack", "dataBinning", "diffPatternTest", "diffPatternTestExon", "exonTrack", "normFactor", "plotTest", "plotTrack", "psiteCal", "psiteMapping", "RiboDiPA" ], "_datasets": [ { "name": "data.binned", "title": "An example of binned P-sites data", "object": "data.binned", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "data.psite", "title": "An example of P-site coverage data", "object": "data.psite", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "result.exon", "title": "An example of exon-level differential pattern analysis result", "object": "result.exon", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "result.pst", "title": "An example of differential pattern analysis result", "object": "result.pst", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "binTrack", "title": "Visualization: generating tracks for 'igvR' (per bin)", "topics": [ "binTrack" ] }, { "page": "bpTrack", "title": "Visualization: generating tracks for 'igvR' (per bp)", "topics": [ "bpTrack" ] }, { "page": "data.binned", "title": "An example of binned P-sites data", "topics": [ "data.binned" ] }, { "page": "data.psite", "title": "An example of P-site coverage data", "topics": [ "data.psite" ] }, { "page": "DataBinning", "title": "Data binning", "topics": [ "dataBinning" ] }, { "page": "diffPatternTest", "title": "Differential pattern analysis of Ribo-seq data", "topics": [ "diffPatternTest" ] }, { "page": "diffPatternTestExon", "title": "Main function for differential pattern analysis of exon-binned Ribo-seq data", "topics": [ "diffPatternTestExon" ] }, { "page": "exonTrack", "title": "Visualization: generating tracks for 'igvR' (per exon)", "topics": [ "exonTrack" ] }, { "page": "normFactor", "title": "Size factors for normalization by sequencing depth", "topics": [ "normFactor" ] }, { "page": "plotTest", "title": "Plotting ribosome footprint data from mapped P-sites at the bin level.", "topics": [ "plotTest" ] }, { "page": "plotTrack", "title": "Plotting ribosome footprint data at the mapped P-site level", "topics": [ "plotTrack" ] }, { "page": "psitecal", "title": "P-site position of reads", "topics": [ "psiteCal" ] }, { "page": "PsiteMapping", "title": "P-site mapping", "topics": [ "psiteMapping" ] }, { "page": "result.exon", "title": "An example of exon-level differential pattern analysis result", "topics": [ "result.exon" ] }, { "page": "result.pst", "title": "An example of differential pattern analysis result", "topics": [ "result.pst" ] }, { "page": "RiboDiPA", "title": "A wrapper function for the RiboDiPA pipeline", "topics": [ "RiboDiPA" ] } ], "_readme": "https://github.com/bioc/RiboDiPA/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "backports", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "callr", "checkmate", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "densEstBayes", "desc", "DESeq2", "distributional", "doParallel", "dplyr", "elitism", "farver", "fastmap", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "hms", "httr", "httr2", "inline", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "locfit", "loo", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "numDeriv", "openssl", "otel", "pillar", "pkgbuild", "pkgconfig", "plyr", "png", "posterior", "prettyunits", "processx", "progress", "ps", "purrr", "QuickJSR", "qvalue", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "RCurl", "reldist", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rstan", "rstantools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "StanHeaders", "stringi", "stringr", "SummarizedExperiment", "sys", "tensorA", "tibble", "tidyr", "tidyselect", "txdbmaker", "UCSC.utils", "utf8", "vctrs", "viridisLite", "withr", "XML", "xml2", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "RiboDiPA.Rmd", "filename": "RiboDiPA.html", "title": "RiboDiPA R package", "author": "Keren Li, Matthew Hope, Xiaozhong A. Wang, Ji-Ping Wang", "engine": "knitr::rmarkdown", "headings": [ "Maintainer: Ji-Ping Wang, ", "What is RiboDiPA?", "RiboDiPA pipeline", "Installation", "Input files", "RiboDiPA main features", "The RiboDiPA pipeline", "0. Ribo-DiPA Wrapper Function", "1. P-site mapping", "2. Data binning", "3. Differential pattern analysis", "4. Plotting and genome visualization", "Individual gene plotting", "Track plotting via genome browser", "Conclusion", "Session info" ], "created": "2020-04-20 23:52:21", "modified": "2021-12-29 20:08:47", "commits": 12 } ], "_score": 4, "_indexed": true, "_nocasepkg": "ribodipa", "_universes": [ "bioc", "jipingw" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-06-18T11:29:58.000Z", "distro": "noble", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "9cb903c1c73e918c488fa5069c5b12888ee785133c53239cb7f6ee119be88405", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-06-18T11:30:57.000Z", "distro": "noble", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "cca780af99fa988ad5ec52f4713c77f382eb51ce64473f82b28f069c380ed645", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-06-18T11:30:18.000Z", "distro": "noble", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "1c62a00fb99447910db5a95f4a7f5224e7aba27ec1afa8bb8ffa5dc8edee48c7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-06-18T11:30:59.000Z", "distro": "noble", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "4ab0286ec055b487482231d8802605cced6a38450274ba4cd68c8f6cb10c2028", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-06-18T11:32:24.000Z", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "56b3211c6053c04ff41dc5d1b629b0f62b0589d002580d094e05590f98887097", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-06-18T11:32:21.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "ee835e4ddc4010057995988a4ffad4f739e1d566ca013447280134c3270013d5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-06-18T11:32:43.000Z", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "1276a23a2f74387d60e2b18b6e953a9a11da26e617fee6fc0b060ea5c2be6db3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-06-18T11:33:41.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "901a2fc0b250e6dd98ede02234ed1c18cd55fdbb8db67b151a947d723bfd2088", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-06-18T11:30:27.000Z", "arch": "emscripten", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "1b68850214f29b898b9ffbff3ec86f63299ef36c868d7c2d4d8c14bdd6bbfe24", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-06-18T11:29:50.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "297ba9c63d10299b3a70bbf31e409836cade7e12a73a71dece6859bdbf53019f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-06-18T11:28:50.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "b9ebef82c7d8ce4a187dd61368c7c2e35f0e57df915e9ade6199087da9b36d7f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-06-18T11:28:58.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "60a677c4d9a1b3c41f6e38d034a1e899f0ef2cfc84a991112a969144ebe78991", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27755761062" } ] }