# An integrative R package for analysing alternative splicing using RNAseq
Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz
Alternative splicing (AS) is a common mechanism of post-transcriptional gene
regulation in eukaryotic organisms that expands the functional and regulatory
diversity of a single gene by generating multiple mRNA isoforms that encode
structurally and functionally distinct proteins. The development of novel
high-throughput sequencing methods for RNA (RNAseq) has provided a powerful
means of studying AS under multiple conditions and in a genome-wide manner.
However, using RNAseq to study changes in AS under different experimental
conditions is not trivial.
In this vignette, we describe how to use ASpli, an integrative and user-friendly
R package that facilitates the analysis of changes in both annotated and novel
AS events. This package combines statistical information from exon, intron, and
splice junction differential usage (p-value, FDR), with information from splice
junction reads to calculate differences in the percentage of exon inclusion
Delta-PSI and intron retention Delta-PIR). The proposed methodology
reliably reflect the magnitude of changes in the relative abundance of different
annotated and novel AS events. This method can be used to analyze both simple
and complex experimental designs involving multiple experimental conditions.
## Getting started
ASpli is available at Bioconductor site and can be downloaded using
**biocLite()** will take care of installing all the packages that ASpli
depends on e.g. edgeR, GenomicFeatures, GenomicRanges, GenomicAlignments, Gviz,
and other R package required. Some packages depend on operating system
packages, like **curl**, that are not installed automatically, and should
be installed by the user.