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SpliceWiz

Easy, optimized, and accurate alternative splicing analysis in R


Bioconductor version: Release (3.18)

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.

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")

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 1.4.1
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, 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
System Requirements C++11, GNU make
URL https://github.com/alexchwong/SpliceWiz
Bug Reports https://support.bioconductor.org/
See More
Suggests knitr, rmarkdown, openssl, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea, Rsubread
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_1.4.1.tar.gz
Windows Binary SpliceWiz_1.4.1.zip
macOS Binary (x86_64) SpliceWiz_1.4.1.tgz
macOS Binary (arm64) SpliceWiz_1.4.1.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 3.18 Source Archive