EventPointer

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see EventPointer.

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


Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EventPointer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EventPointer")
EventPointer HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, DifferentialSplicing, RNASeq, Sequencing, Software, Transcription, mRNAMicroarray
Version 1.4.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
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
System Requirements
URL
Bug Reports https://github.com/jpromeror/EventPointer/issues
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Suggests knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
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Package Archives

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

Source Package EventPointer_1.4.0.tar.gz
Windows Binary EventPointer_1.4.0.zip
Mac OS X 10.11 (El Capitan) EventPointer_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EventPointer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EventPointer
Package Short Url https://bioconductor.org/packages/EventPointer/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive