{ "_id": "6a1aae041d7bb097a09d4e2a", "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": "2026-05-30 06:58:27 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": "23c1d8161699f0a9be7582798c46464f", "_user": "bioc", "_type": "src", "_file": "RiboDiPA_1.21.0.tar.gz", "_fileid": "2a9749b054e24c93ff0c51baf8d47cb3f1d18bbc0ab25dbb02322a0a0628c244", "_filesize": 1839814, "_sha256": "2a9749b054e24c93ff0c51baf8d47cb3f1d18bbc0ab25dbb02322a0a0628c244", "_created": "2026-05-30T06:58:27.000Z", "_published": "2026-05-30T09:29:40.110Z", "_jobs": [ { "job": 78631925614, "time": 232, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306295441" }, { "job": 78631925623, "time": 671, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306347348" }, { "job": 78631925621, "time": 824, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306364380" }, { "job": 78631925625, "time": 693, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7306349798" }, { "job": 78631925622, "time": 775, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306358975" }, { "job": 78631925648, "time": 481, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307117696" }, { "job": 78631925645, "time": 1095, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7306565324" }, { "job": 78631925620, "time": 654, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7307135105" }, { "job": 78631925627, "time": 1198, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306579010" }, { "job": 78631412858, "time": 581, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306267144" }, { "job": 78631925615, "time": 183, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306289416" }, { "job": 78631925624, "time": 800, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306362048" }, { "job": 78631925616, "time": 843, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306366623" }, { "job": 78631925618, "time": 830, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306365255" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677298091", "_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", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 351, "source": "https://www.bioconductor.org/packages/stats/bioc/RiboDiPA" }, "_searchresults": 2, "_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", "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": "2026-04-30T15:34:49.000Z", "distro": "noble", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "d5352f7565f9a151f268e794006b55a6045dfbb9007c64f1d49f511a8ac0c6e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-04-30T15:40:08.000Z", "distro": "noble", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "55c0c32bc8027c7b6c41955d1e42e5ca36e3fb4b135947e054fd7ac3806cc5c9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-04-30T15:34:12.000Z", "distro": "noble", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "b2e251fe5c242c9900575611e42d1fae8ee44563f00db092f4e5e04e09af98e5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-04-30T15:42:24.000Z", "distro": "noble", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "481b27e867760b8c92e78ecf40c241eb152c7998d41f57a82a0a929ff1365929", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-04-30T17:12:41.000Z", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "bb96cbd8004de20701361a56b4d77d8732ab63d5627c6c405bc49058758f6fec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-04-30T16:14:25.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "dbd21ae0a6f8bc29b9fa760a89e006cfadb070c0b3bbd3aaa3042e138635c983", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-04-30T17:12:28.000Z", "arch": "aarch64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "77ae7c68cabca264d3dea6ba9fefa2972857207bf80db37e7bbcb0ef7854de06", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-04-30T16:16:35.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "b8e6a92fa64424dc825de3a6060ea5aa2cc89de64b6619f8014949ba5746b020", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-04-30T15:39:54.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "41ddd6320bd9a3a297bf766fe89d8d3745240193a143e38424e701c76ec2a531", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-04-30T15:38:10.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "6566614182ff8080dee9d1b43082b6d4e187d6051af5016ab06cab085975b14c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-04-30T15:38:40.000Z", "arch": "x86_64", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "4956bf46d21f6ea23fc2c1d356159c9f3569f1ad75a5e6b10fe7c854b6986dfc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-22T21:03:45.000Z", "arch": "emscripten", "commit": "3960dad2f262421f3ab8e6db449d9f1530a5b408", "fileid": "75594082a01813b6bb806f840fc95ba6309c03eb228f907af156003d6ae8868a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173644615" } ] }