{ "_id": "6a1af4e51d7bb097a09f8f95", "Package": "SpliceWiz", "Title": "interactive analysis and visualization of alternative splicing\nin R", "Version": "1.15.0", "Date": "2025-03-13", "Authors@R": "c(person(\"Alex Chit Hei\", \"Wong\", email=\"alexchwong.github@gmail.com\", \nrole=c(\"aut\", \"cre\", \"cph\")),\nperson(\"Ulf\", \"Schmitz\", role=c(\"ctb\")),\nperson(\"William\", \"Ritchie\", role=c(\"cph\")))", "Description": "The analysis and visualization of alternative splicing\n(AS) events from RNA sequencing data remains challenging.\nSpliceWiz is a user-friendly and performance-optimized R\npackage for AS analysis, by processing alignment BAM files to\nquantify read counts across splice junctions, IRFinder-based\nintron retention quantitation, and supports novel splicing\nevent identification. We introduce a novel visualization for AS\nusing normalized coverage, thereby allowing visualization of\ndifferential AS across conditions. SpliceWiz features a\nshiny-based GUI facilitating interactive data exploration of\nresults including gene ontology enrichment. It is performance\noptimized with multi-threaded processing of BAM files and a new\nCOV file format for fast recall of sequencing coverage.\nOverall, SpliceWiz streamlines AS analysis, enabling reliable\nidentification of functionally relevant AS events for further\ncharacterization.", "License": "MIT + file LICENSE", "SystemRequirements": "C++11, GNU make", "Collate": "AllImports.R RcppExports.R zzz.R AllClasses.R AllGenerics.R\nASEFilter-methods.R NxtSE-methods.R globals.R ggplot_themes.R\nexample_data.R wrappers.R make_plot_data.R Coverage.R\ncovPlotly-methods.R covDataObject-methods.R\ncovPlotObject-methods.R plotCoverage.R utils.R File_finders.R\nBuildRef_GO.R BuildRef.R ViewRef.R STAR_utils.R Mappability.R\nProcessBAM_docs.R ProcessBAM.R CollateData.R MakeSE.R Filters.R\nASE-methods.R ASE-GLM-edgeR.R dash_filterModules.R\ndash_globals.R dash_settings.R dash_ref_new_ui.R\ndash_ref_new_server.R dash_expr_ui.R dash_expr_server.R\ndash_QC.R dash_filters.R dash_DE_ui.R 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09:42:38 UTC", "User": "root" }, "Author": "Alex Chit Hei Wong [aut, cre, cph],\nUlf Schmitz [ctb],\nWilliam Ritchie [cph]", "Maintainer": "Alex Chit Hei Wong ", "MD5sum": "a8555f6dadafde21877098828d12c134", "_user": "bioc", "_type": "src", "_file": "SpliceWiz_1.15.0.tar.gz", "_fileid": "399e2cefc915837678de3be13189504aa45015b0dbc66ddf353f8b8d768a7714", "_filesize": 4788217, "_sha256": "399e2cefc915837678de3be13189504aa45015b0dbc66ddf353f8b8d768a7714", "_created": "2026-05-30T09:42:38.000Z", "_published": "2026-05-30T14:32:05.145Z", "_jobs": [ { "job": 78640461153, "time": 309, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307447122" }, { "job": 78640461150, "time": 677, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7307338158" }, { "job": 78640461155, "time": 1014, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307507687" }, { "job": 78640461154, "time": 730, "config": "linux-release-arm64", "r": 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"source": "SW_QuickStart.Rmd", "filename": "SW_QuickStart.html", "title": "SpliceWiz: Quick Start", "author": "Alex CH Wong", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "FAQ", "Workflow from a glance", "Quick-Start", "Installation", "Loading SpliceWiz", "The SpliceWiz Graphics User Interface (GUI)", "Navigating the GUI", "Building the SpliceWiz reference", "Process BAM files using SpliceWiz", "Collate the experiment", "Importing the experiment", "Differential analysis", "Assigning annotations to samples", "Filtering high-confidence events", "Performing differential analysis", "Visualization", "Volcano plots", "Scatter plots", "Gene ontology (GO) analysis", "Heatmaps", "SpliceWiz Coverage Plots", "Coverage plots of individual samples", "Normalized Coverage plots of individual samples", "Group Coverage plots", "Coverage plots using exon windows", "Using the GUI", "SessionInfo" ], "created": "2022-05-11 23:24:23", "modified": "2024-03-12 08:26:36", "commits": 27 }, { 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