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README.md
# 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 3.16 / R 4.2) <a name="docorelease"></a> [Bioconductor Landing Page (Release - 3.16)](https://bioconductor.org/packages/release/bioc/html/SpliceWiz.html) [QuickStart Vignette (Release - 3.16)](https://bioconductor.org/packages/release/bioc/vignettes/SpliceWiz/inst/doc/SW_QuickStart.html) [Reference Manual (Release - 3.16)](https://bioconductor.org/packages/release/bioc/manuals/SpliceWiz/man/SpliceWiz.pdf) ## Bioconductor Devel (Bioc 3.17 / R 4.3) <a name="docodevel"></a> [Bioconductor Landing Page (Devel - 3.17)](https://bioconductor.org/packages/devel/bioc/html/SpliceWiz.html) [QuickStart Vignette (Devel - 3.17)](https://bioconductor.org/packages/devel/bioc/vignettes/SpliceWiz/inst/doc/SW_QuickStart.html) [Reference Manual (Devel - 3.17)](https://bioconductor.org/packages/devel/bioc/manuals/SpliceWiz/man/SpliceWiz.pdf) # Installation (Release - Bioc 3.16 / R 4.2) <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 >= 4.2.0) using Bioconductor version 3.16 (current release) <a name="instrelease"></a> ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.16") BiocManager::valid() # checks for out of date packages BiocManager::install("SpliceWiz") ``` ## On R (devel version >= 4.3) using Bioconductor version 3.17 (devel) <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= TRUE)) install.packages("BiocManager") BiocManager::install(version = "devel") BiocManager::valid() # checks for out of date packages BiocManager::install("SpliceWiz") ``` ## Installing via GitHub 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 3.15 or earlier ``` library("devtools") install_github("alexchwong/ompBAM") # to install SpliceWiz version 1.1.6, install from the "1.1.6-release" branch: install_github("alexchwong/SpliceWiz", "1.1.6-release", 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> Check out our (latest) pre-print publication for SpliceWiz: [SpliceWiz: easy, optimized, and accurate alternative splicing analysis in R](https://www.biorxiv.org/content/10.1101/2022.07.05.498887v1)