# SpliceWiz
SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.
# Table of Contents
1. [Documentation](#doco)
1. [Bioconductor Release](#docorelease)
2. [Bioconductor Devel](#docodevel)
2. [Installation](#inst)
1. [Enabling OpenMP (MacOS)](#ompmac)
2. [Installation for Bioconductor (current release)](#instrelease)
3. [Installation for Bioconductor (devel)](#instdevel)
4. [Installing via GitHub](#instlegacy)
3. [Publication](#pub)
# Documentation <a name="doco"></a>
## Bioconductor Release (Bioc 3.18 / R 4.3) <a name="docorelease"></a>
[Bioconductor Landing Page (Release)](https://bioconductor.org/packages/release/bioc/html/SpliceWiz.html)
[QuickStart Vignette (Release)](https://bioconductor.org/packages/release/bioc/vignettes/SpliceWiz/inst/doc/SW_QuickStart.html)
[Reference Manual (Release)](https://bioconductor.org/packages/release/bioc/manuals/SpliceWiz/man/SpliceWiz.pdf)
## Bioconductor Devel (future Bioc 3.19 / R 4.3) <a name="docodevel"></a>
[Bioconductor Landing Page (Devel)](https://bioconductor.org/packages/devel/bioc/html/SpliceWiz.html)
[QuickStart Vignette (Devel)](https://bioconductor.org/packages/devel/bioc/vignettes/SpliceWiz/inst/doc/SW_QuickStart.html)
[Reference Manual (Devel)](https://bioconductor.org/packages/devel/bioc/manuals/SpliceWiz/man/SpliceWiz.pdf)
# Installation (Release - Bioc 3.18 / R 4.3) <a name="inst"></a>
## Enabling OpenMP multi-threading (for MacOS users) <a name="ompmac"></a>
OpenMP is installed by default on Windows and Linux systems. For MacOS, OpenMP
is not officially supported. To install SpliceWiz with OpenMP support, first
install the `libomp` libraries via brew:
```
brew install libomp
```
## On R (version >= 4.3) using Bioconductor version 3.18 (current release) <a name="instrelease"></a>
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.18")
BiocManager::valid() # checks for out of date packages
BiocManager::install("SpliceWiz")
```
## On R-devel using Bioconductor devel (future 3.19) <a name="instdevel"></a>
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "devel")
BiocManager::valid() # checks for out of date packages
BiocManager::install("SpliceWiz")
```
## Installing via GitHub <a name="instlegacy"></a>
Reasons for installing via GitHub:
* Using the latest development version on current release of Bioconductor -
means you don't have to install Bioconductor devel
* You are using Bioconductor version 3.16 or earlier
```
library("devtools")
install_github("alexchwong/ompBAM")
# To install the latest devel version, install from the "main" branch
install_github("alexchwong/SpliceWiz", "main", dependencies=TRUE)
```
Note that prior to Bioconductor versions 3.14 or earlier, you may need to retrieve
Mappability files from https://github.com/alexchwong/SpliceWizResources
# Publication <a name="pub"></a>
SpliceWiz is now published!
[SpliceWiz: interactive analysis and visualization of alternative splicing in R](https://academic.oup.com/bib/article/25/1/bbad468/7502685)
