SpliceWiz

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SpliceWiz.

Easy, optimized, and accurate alternative splicing analysis in R


Bioconductor version: 3.16

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>

Citation (from within R, enter citation("SpliceWiz")):

Installation

To install this package, start R (version "4.2") 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")
SpliceWiz: Quick Start HTML R Script
SpliceWiz: the cookbook HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, GUI, RNASeq, Sequencing, Software, Transcriptomics
Version 1.0.4
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), NxtIRFdata
Imports ompBAM, methods, stats, utils, tools, parallel, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, IRanges, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, rhandsontable, DT, grDevices, heatmaply, pheatmap, matrixStats, RColorBrewer, XML
System Requirements C++11
URL https://github.com/alexchwong/SpliceWiz
Bug Reports https://support.bioconductor.org/
See More
Suggests knitr, rmarkdown, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, satuRn, edgeR, Rsubread, testthat (>= 3.0.0)
Linking To ompBAM, Rcpp, zlibbioc, RcppProgress
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SpliceWiz_1.0.4.tar.gz
Windows Binary SpliceWiz_1.0.4.zip
macOS Binary (x86_64) SpliceWiz_1.0.4.tgz
macOS Binary (arm64) SpliceWiz_1.0.4.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 3.16 Source Archive