Package: SpliceWiz
Title: interactive analysis and visualization of alternative splicing
        in R
Version: 1.6.6
Date: 2024-10-13
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, 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
git_url: https://git.bioconductor.org/packages/SpliceWiz
git_branch: RELEASE_3_19
git_last_commit: 224053d
git_last_commit_date: 2024-10-12
Repository: Bioconductor 3.19
Date/Publication: 2024-10-16
NeedsCompilation: yes
Packaged: 2024-10-17 02:16:22 UTC; biocbuild
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 4.4.1; x86_64-w64-mingw32; 2024-10-17 12:43:07 UTC; windows
Archs: x64
