To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("EventPointer")

In most cases, you don't need to download the package archive at all.

EventPointer

DOI: 10.18129/B9.bioc.EventPointer    

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

Bioconductor version: Release (3.5)

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>

Citation (from within R, enter citation("EventPointer")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("EventPointer")

Documentation

HTML R Script EventPointer
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, DifferentialSplicing, RNASeq, Sequencing, Software, Transcription, mRNAMicroarray
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
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
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
BugReports https://github.com/jpromeror/EventPointer/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source EventPointer_1.0.0.tar.gz
Windows Binary EventPointer_1.0.0.zip
Mac OS X 10.11 (El Capitan) EventPointer_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EventPointer
Package Short Url http://bioconductor.org/packages/EventPointer/
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