SpliceWiz

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see SpliceWiz.

interactive analysis and visualization of alternative splicing in R

Bioconductor version: 3.19

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 "4.4") 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 1.6.6

In Bioconductor since BioC 3.16 (R-4.2) (2 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, 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_1.6.6.tar.gz

Windows Binary (x86_64) SpliceWiz_1.6.6.zip

macOS Binary (x86_64) SpliceWiz_1.6.6.tgz

macOS Binary (arm64) SpliceWiz_1.6.6.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 3.19 Source Archive