Package: SpliceWiz
Title: Easy, optimized, and accurate alternative splicing analysis in R
Version: 1.1.8
Date: 2023-04-17
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: 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, crayon, splines, testthat (>= 3.0.0), 
    DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea, Rsubread 
LinkingTo: 
    ompBAM,
    Rcpp,
    zlibbioc, 
	RcppProgress,
    Rhtslib (>= 1.13.1)    
SystemRequirements:
    C++11, GNU make,
    libbz2 & liblzma & libcurl (with header files)
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
    ProcessBAM_hts.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
