{ "_id": "6a13f2e0acfb0bcc41d31dda", "Package": "RNAsense", "Type": "Package", "Title": "Analysis of Time-Resolved RNA-Seq Data", "Version": "1.26.0", "Authors@R": "c(person(\"Marcus\", \"Rosenblatt\", email = \"marcus.rosenblatt@gmail.com\", role = \"cre\"),\nperson(\"Gao\", \"Meijang\", role = \"aut\"),\nperson(\"Helge\", \"Hass\", role = \"aut\"),\nperson(\"Daria\", \"Onichtchouk\", role = \"aut\"))", "Description": "RNA-sense tool compares RNA-seq time curves in two\nexperimental conditions, i.e. wild-type and mutant, and works\nin three steps. At Step 1, it builds expression profile for\neach transcript in one condition (i.e. wild-type) and tests if\nthe transcript abundance grows or decays significantly. Dynamic\ntranscripts are then sorted to non-overlapping groups (time\nprofiles) by the time point of switch up or down. At Step 2,\nRNA-sense outputs the groups of differentially expressed\ntranscripts, which are up- or downregulated in the mutant\ncompared to the wild-type at each time point. At Step 3,\nCorrelations (Fisher's exact test) between the outputs of Step\n1 (switch up- and switch down- time profile groups) and the\noutputs of Step2 (differentially expressed transcript groups)\nare calculated. The results of the correlation analysis are\nprinted as two-dimensional color plot, with time profiles and\ndifferential expression groups at y- and x-axis, respectively,\nand facilitates the biological interpretation of the data.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "6.1.1", "BugReports": "https://github.com/marcusrosenblatt/RNAsense", "biocViews": "RNASeq, GeneExpression, DifferentialExpression", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:51:23 UTC", "RemoteUrl": "https://github.com/bioc/RNAsense", "RemoteRef": "RELEASE_3_23", "RemoteSha": "c8168cea7002ffa2d180b920c92821ae334d1fca", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 06:43:45 UTC", "User": "root" }, "Author": "Marcus Rosenblatt [cre],\nGao Meijang [aut],\nHelge Hass [aut],\nDaria Onichtchouk [aut]", "Maintainer": "Marcus Rosenblatt ", "MD5sum": "438d7d15dfe863e53012ffdde0e761f9", "_user": "bioc-release", "_type": "src", "_file": "RNAsense_1.26.0.tar.gz", "_fileid": "25d2300cce5d3cc997c5c953d83c0806ecf11b8842dc57a90475f50e53842bd3", "_filesize": 1105779, "_sha256": "25d2300cce5d3cc997c5c953d83c0806ecf11b8842dc57a90475f50e53842bd3", "_created": "2026-05-25T06:43:45.000Z", "_published": "2026-05-25T06:57:36.028Z", "_jobs": [ { "job": 77668641286, "time": 136, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7193097486" }, { "job": 77668641292, "time": 687, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7193217082" }, { "job": 77668641308, "time": 780, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7193237840" }, { "job": 77668641280, "time": 360, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7193145396" }, { "job": 77668641274, "time": 393, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7193152986" }, { "job": 77667877592, "time": 413, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7193066816" }, { "job": 77668641285, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7193095038" }, { "job": 77668641304, "time": 744, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7193229325" }, { "job": 77668641302, "time": 749, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7193230696" }, { "job": 77668641282, "time": 721, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7193224420" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RNAsense", "_commit": { "id": "c8168cea7002ffa2d180b920c92821ae334d1fca", "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": 1777380683 }, "_maintainer": { "name": "Marcus Rosenblatt", "email": "marcus.rosenblatt@gmail.com", "login": "marcusrosenblatt", "description": "I am interested in music, chess, volleyball and systems biology...", "uuid": 14975596 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "NBPSeq", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "rnaseq", "geneexpression", "differentialexpression" ], "_stars": 1, "_contributors": [ { "user": "marcusrosenblatt", "count": 57, "uuid": 14975596 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 336, "source": "https://www.bioconductor.org/packages/stats/bioc/RNAsense" }, "_devurl": "https://github.com/marcusrosenblatt/rnasense", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/RNAsense.html", "manual.pdf" ], "_homeurl": "https://github.com/marcusrosenblatt/rnasense", "_realowner": "bioc", "_cranurl": false, "_exports": [ "combineResults", "getFC", "getSwitch", "outputGeneTables", "plotSSGS" ], "_datasets": [ { "name": "MZsox", "title": "Time resolved RNA seq data for early zygotic development of zebra fish.", "object": "MZsox", "file": "MZsox.RData", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "combineResults", "title": "Combine results", "topics": [ "combineResults" ] }, { "page": "getFC", "title": "Detect fold changes", "topics": [ "getFC" ] }, { "page": "getSwitch", "title": "Detect switching genes", "topics": [ "getSwitch" ] }, { "page": "MZsox", "title": "Time resolved RNA seq data for early zygotic development of zebra fish.", "topics": [ "MZsox" ] }, { "page": "outputGeneTables", "title": "Output gene tables", "topics": [ "outputGeneTables" ] }, { "page": "plotSSGS", "title": "plot SSGS gene classes", "topics": [ "plotSSGS" ] } ], "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "NBPSeq", "plyr", "qvalue", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "example.Rmd", "filename": "example.html", "title": "RNAsense", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Step-by-step Tutorial", "Session Info" ], "created": "2019-08-03 11:00:29", "modified": "2019-10-22 12:19:52", "commits": 14 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "rnasense", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/RNAsense", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.26.0", "date": "2026-05-25T06:47:26.000Z", "distro": "noble", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "08b360fd311b35a56cacbbb5a685e185f8e906fe0d5e75c60c7b5d902f1fac09", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" }, { "r": "4.6.0", "os": "linux", "version": "1.26.0", "date": "2026-05-25T06:47:16.000Z", "distro": "noble", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "384a648b4f14ff2e2d759a984fee23ef04db9e2a1088de42deac2d452c5356f7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" }, { "r": "4.5.3", "os": "mac", "version": "1.26.0", "date": "2026-05-25T06:45:23.000Z", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "78b133d8d3a9111c400d273fb4a420f700af5d184a25ae05b3ef483dcf2dfb91", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" }, { "r": "4.6.0", "os": "mac", "version": "1.26.0", "date": "2026-05-25T06:45:19.000Z", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "fb874857139fd4acf80df2f6a0c687707157312892f3d9a693c5b602e92ab562", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" }, { "r": "4.6.0", "os": "wasm", "version": "1.26.0", "date": "2026-05-25T06:46:17.000Z", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "86f0a7e3f89a0dc5f2fea12fe8018ad51f7aabb682e65b65582bc9a133dd756e", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" }, { "r": "4.7.0", "os": "win", "version": "1.26.0", "date": "2026-05-25T06:45:21.000Z", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "7cb4eb863f5183c5920dee7657c57a698133e6054560b4184408d6322cd28b8a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" }, { "r": "4.5.3", "os": "win", "version": "1.26.0", "date": "2026-05-25T06:45:09.000Z", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "685bc8a9493aff7b8f78d26ef78fb265339a715f8e77ab52b1b377802fc485ca", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" }, { "r": "4.6.0", "os": "win", "version": "1.26.0", "date": "2026-05-25T06:45:14.000Z", "commit": "c8168cea7002ffa2d180b920c92821ae334d1fca", "fileid": "73d94cb6bbabdc76c675a17fd60be085f9d832c20af52c65482933590b1b492f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26387063684" } ] }