SpliceWiz

DOI: 10.18129/B9.bioc.SpliceWiz  

Easy, optimized, and accurate alternative splicing analysis in R

Bioconductor version: Release (3.17)

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.

Author: Alex Chit Hei Wong [aut, cre, cph], Ulf Schmitz [ctb], William Ritchie [cph]

Maintainer: Alex Chit Hei Wong <a.wong at centenary.org.au>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SpliceWiz")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpliceWiz")

 

HTML	R Script	SpliceWiz: Quick Start
HTML	R Script	SpliceWiz: the cookbook
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, GUI, RNASeq, Sequencing, Software, Transcriptomics
Version	1.2.3
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
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
LinkingTo	ompBAM, Rcpp, zlibbioc, RcppProgress
Suggests	knitr, rmarkdown, openssl, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea, Rsubread
SystemRequirements	C++11, GNU make
Enhances
URL	https://github.com/alexchwong/SpliceWiz
BugReports	https://support.bioconductor.org/
Depends On Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SpliceWiz_1.2.3.tar.gz
Windows Binary	SpliceWiz_1.2.3.zip
macOS Binary (x86_64)	SpliceWiz_1.2.3.tgz
macOS Binary (arm64)	SpliceWiz_1.2.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpliceWiz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SpliceWiz
Bioc Package Browser	https://code.bioconductor.org/browse/SpliceWiz/
Package Short Url	https://bioconductor.org/packages/SpliceWiz/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive