SpliceWiz

This is the released version of SpliceWiz; for the devel version, see SpliceWiz.

interactive analysis and visualization of alternative splicing in R

Bioconductor version: Release (3.21)

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 <alexchwong.github at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, GUI, RNASeq, Sequencing, Software, Transcriptomics
Version	1.10.0
In Bioconductor since	BioC 3.16 (R-4.2) (2.5 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, RSQLite, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, h5mread, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr
System Requirements	C++11, GNU make
URL	https://github.com/alexchwong/SpliceWiz
Bug Reports	https://support.bioconductor.org/

Suggests	knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread
Linking To	ompBAM, Rcpp, 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_1.10.0.tar.gz
Windows Binary (x86_64)	SpliceWiz_1.10.0.zip
macOS Binary (x86_64)	SpliceWiz_1.10.0.tgz
macOS Binary (arm64)	SpliceWiz_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SpliceWiz
Source Repository (Developer Access)	git clone [email protected]:packages/SpliceWiz
Bioc Package Browser	https://code.bioconductor.org/browse/SpliceWiz/
Package Short Url	https://bioconductor.org/packages/SpliceWiz/
Package Downloads Report	Download Stats