Package: SpliceWiz
Title: Easy, optimized, and accurate alternative splicing analysis in R
Version: 1.2.2
Date: 2023-06-05
Authors@R: c(person("Alex Chit Hei", "Wong", email="a.wong@centenary.org.au", 
		role=c("aut", "cre", "cph")),
	person("Ulf", "Schmitz", role=c("ctb")),
	person("William", "Ritchie", role=c("cph")))
Description: Reads and fragments aligned to splice junctions can be used to
    quantify alternative splicing events (ASE). However, overlapping ASEs can
	confound their quantification. SpliceWiz quantifies ASEs, calculating
	percent-spliced-in (PSI) using junction reads, and intron retention using
	IRFinder-based quantitation. Novel filters identify ASEs that are relatively
	less confounded by overlapping events, whereby PSIs can be calculated with
	higher confidence. SpliceWiz is ultra-fast, using multi-threaded processing
	of BAM files. It can be run using a graphical user or command line 
	interfaces. GUI-based interactive visualization of differential ASEs,
	including novel group-based RNA-seq coverage visualization, simplifies
	short-read RNA-seq analysis in R.
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, 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
Suggests: knitr, rmarkdown, openssl, crayon, splines, testthat (>=
        3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea,
        Rsubread
LinkingTo: ompBAM, Rcpp, zlibbioc, 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: 7.2.3
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_17
git_last_commit: f690f49
git_last_commit_date: 2023-06-04
Date/Publication: 2023-06-05
NeedsCompilation: yes
Packaged: 2023-06-05 22:37:10 UTC; biocbuild
Author: Alex Chit Hei Wong [aut, cre, cph],
  Ulf Schmitz [ctb],
  William Ritchie [cph]
Maintainer: Alex Chit Hei Wong <a.wong@centenary.org.au>
Built: R 4.3.1; x86_64-conda-linux-gnu; 2023-07-15 23:58:34 UTC; unix
