DOI: 10.18129/B9.bioc.EventPointer    

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

Bioconductor version: Release (3.6)

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). 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.

Author: Juan Pablo Romero, Ander Muniategui, Fernando Carazo, Ander Aramburu, Angel Rubio

Maintainer: Juan Pablo Romero <jpromero at ceit.es>

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biocViews AlternativeSplicing, DifferentialSplicing, RNASeq, Sequencing, Software, Transcription, mRNAMicroarray
Version 1.2.0
In Bioconductor since BioC 3.5 (R-3.4) (1 year)
License Artistic-2.0
Depends R (>= 3.4), SGSeq, Matrix, SummarizedExperiment
Imports GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors
Suggests knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
BugReports https://github.com/jpromeror/EventPointer/issues
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