|
|
|
|
|
|
|
This is the development version of SpliceWiz; for the stable release version, see SpliceWiz.
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")
):
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.
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 |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
Follow Installation instructions to use this package in your R session.
Source Package | SpliceWiz_1.1.6.tar.gz |
Windows Binary | SpliceWiz_1.1.6.zip |
macOS Binary (x86_64) | SpliceWiz_1.1.6.tgz |
macOS Binary (arm64) | SpliceWiz_1.1.5.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 |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: