EventPointer
Bioc currentAn effective identification of alternative splicing events using junction arrays and RNA-Seq data
Release Lineage
Entered 3.5 · Apr 25, 2017
Current · Requires R 4.6
Description
EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). In the latter, EventPointer can work with annotated splicing events or can build a splicing graph from the RNA-Seq reads and then identify new and specific alternative splicing events. The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.
Code
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Topics
People
- Juan A. Ferrer-Bonsoms author maintainer
- Ander Aramburu author
- Fernando Carazo author
- Ander Muniategui author
- Juan Pablo Romero author
- Angel Rubio author
- Pablo Sacristan author