SpliceWiz

DOI: 10.18129/B9.bioc.SpliceWiz    

This is the development version of SpliceWiz; for the stable release version, see SpliceWiz.

Easy, optimized, and accurate alternative splicing analysis in R

Bioconductor version: Development (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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.2
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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
LinkingTo ompBAM, Rcpp, zlibbioc, RcppProgress
Suggests knitr, rmarkdown, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, satuRn, splines, edgeR, Rsubread, testthat (>= 3.0.0)
SystemRequirements C++11
Enhances
URL https://github.com/alexchwong/SpliceWiz
BugReports https://support.bioconductor.org/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package SpliceWiz_1.1.2.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SpliceWiz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpliceWiz
Package Short Url https://bioconductor.org/packages/SpliceWiz/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: