Package: SpliceWiz
Title: interactive analysis and visualization of alternative splicing
        in R
Version: 1.13.0
Date: 2025-03-13
Authors@R: c(person("Alex Chit Hei", "Wong", email="alexchwong.github@gmail.com", 
		role=c("aut", "cre", "cph")),
	person("Ulf", "Schmitz", role=c("ctb")),
	person("William", "Ritchie", role=c("cph")))
Description: The analysis and visualization of alternative splicing
        (AS) events from RNA sequencing data remains challenging.
        SpliceWiz is a user-friendly and performance-optimized R
        package for AS analysis, by processing alignment BAM files to
        quantify read counts across splice junctions, IRFinder-based
        intron retention quantitation, and supports novel splicing
        event identification. We introduce a novel visualization for AS
        using normalized coverage, thereby allowing visualization of
        differential AS across conditions. SpliceWiz features a
        shiny-based GUI facilitating interactive data exploration of
        results including gene ontology enrichment. It is performance
        optimized with multi-threaded processing of BAM files and a new
        COV file format for fast recall of sequencing coverage.
        Overall, SpliceWiz streamlines AS analysis, enabling reliable
        identification of functionally relevant AS events for further
        characterization.
License: MIT + file LICENSE
Depends: R (>= 3.5.0), NxtIRFdata
Imports: ompBAM, methods, stats, utils, tools, parallel, scales,
        magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2,
        AnnotationHub, RSQLite, BiocFileCache, BiocGenerics,
        BiocParallel, Biostrings, BSgenome, DelayedArray,
        DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges,
        HDF5Array, h5mread, htmltools, IRanges, patchwork, pheatmap,
        progress, plotly, R.utils, rhdf5, rtracklayer,
        SummarizedExperiment, S4Vectors, shiny, shinyFiles,
        shinyWidgets, shinydashboard, stringi, rhandsontable, DT,
        grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr
Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0),
        DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi,
        fgsea, Rsubread
LinkingTo: ompBAM, Rcpp, RcppProgress
SystemRequirements: C++11, GNU make
Collate: AllImports.R RcppExports.R zzz.R AllClasses.R AllGenerics.R
        ASEFilter-methods.R NxtSE-methods.R globals.R ggplot_themes.R
        example_data.R wrappers.R make_plot_data.R Coverage.R
        covPlotly-methods.R covDataObject-methods.R
        covPlotObject-methods.R plotCoverage.R utils.R File_finders.R
        BuildRef_GO.R BuildRef.R ViewRef.R STAR_utils.R Mappability.R
        ProcessBAM_docs.R ProcessBAM.R CollateData.R MakeSE.R Filters.R
        ASE-methods.R ASE-GLM-edgeR.R dash_filterModules.R
        dash_globals.R dash_settings.R dash_ref_new_ui.R
        dash_ref_new_server.R dash_expr_ui.R dash_expr_server.R
        dash_QC.R dash_filters.R dash_DE_ui.R dash_DE_server.R
        dash_vis_ui.R dash_vis_server.R dash_cov_ui.R dash_cov_server.R
        dash_GO_ui.R dash_GO_server.R dash_ui.R dash_server.R dash.R
        SpliceWiz-package.R
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: Software, Transcriptomics, RNASeq, AlternativeSplicing,
        Coverage, DifferentialSplicing, DifferentialExpression, GUI,
        Sequencing
URL: https://github.com/alexchwong/SpliceWiz
BugReports: https://support.bioconductor.org/
Config/testthat/edition: 3
Config/pak/sysreqs: make libmagick++-dev gsfonts libbz2-dev libicu-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:17:35 UTC
RemoteUrl: https://github.com/bioc/SpliceWiz
RemoteRef: HEAD
RemoteSha: 73b017ace163dfa33330c511384a28c4d9078877
NeedsCompilation: yes
Packaged: 2025-12-23 08:24:08 UTC; root
Author: Alex Chit Hei Wong [aut, cre, cph],
  Ulf Schmitz [ctb],
  William Ritchie [cph]
Maintainer: Alex Chit Hei Wong <alexchwong.github@gmail.com>
Built: R 4.6.0; x86_64-apple-darwin20; 2025-12-23 08:48:31 UTC; unix
