README.md

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

SpliceWiz

SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.

Table of Contents

1. Documentation
   1. Bioconductor Release
   2. Bioconductor Devel
2. Installation
   1. Enabling OpenMP (MacOS)
   2. Installation for Bioconductor (current release)
   3. Installation for Bioconductor (devel)
   4. Installing via GitHub
3. Publication

Documentation

Bioconductor Release (Bioc 3.18 / R 4.3)

Bioconductor Landing Page (Release)

QuickStart Vignette (Release)

Reference Manual (Release)

Bioconductor Devel (future Bioc 3.19 / R 4.3)

Bioconductor Landing Page (Devel)

QuickStart Vignette (Devel)

Reference Manual (Devel)

Installation (Release - Bioc 3.18 / R 4.3)

Enabling OpenMP multi-threading (for MacOS users)

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)

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BiocManager::valid()              # checks for out of date packages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)

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BiocManager::valid()              # checks for out of date packages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

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

SpliceWiz is now published!

SpliceWiz: interactive analysis and visualization of alternative splicing in R

alexchwong/SpliceWiz documentation built on March 17, 2024, 3:16 a.m.