EventPointer

DOI: 10.18129/B9.bioc.EventPointer    

This package is for version 3.8 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: 3.8

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, Juan Ferrer-Bonsoms, Ander Muniategui, Fernando Carazo, Ander Aramburu, Angel Rubio

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	EventPointer
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, DifferentialSplicing, ImmunoOncology, RNASeq, Sequencing, Software, TimeCourse, Transcription, mRNAMicroarray
Version	2.0.1
In Bioconductor since	BioC 3.5 (R-3.4) (2 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, IRanges, qvalue, cobs, rhdf5
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
BugReports	https://github.com/jpromeror/EventPointer/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	EventPointer_2.0.1.tar.gz
Windows Binary	EventPointer_2.0.1.zip
Mac OS X 10.11 (El Capitan)	EventPointer_2.0.1.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	http://bioconductor.org/packages/EventPointer/
Package Downloads Report	Download Stats