SpliceWiz
Easy, optimized, and accurate alternative splicing analysis in R
Bioconductor version: Release (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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, GUI, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.2.3 |
| In Bioconductor since | BioC 3.16 (R-4.2) (1 year) |
| 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 |
| Linking To | ompBAM, Rcpp, zlibbioc, RcppProgress |
| Suggests | knitr, rmarkdown, openssl, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea, Rsubread |
| System Requirements | C++11, GNU make |
| Enhances | |
| URL | https://github.com/alexchwong/SpliceWiz |
| Bug Reports | https://support.bioconductor.org/ |
See More
| 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_1.2.3.tar.gz |
| Windows Binary | SpliceWiz_1.2.3.zip |
| macOS Binary (x86_64) | SpliceWiz_1.2.3.tgz |
| macOS Binary (arm64) | SpliceWiz_1.2.2.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 3.17 | Source Archive |