EventPointer

DOI: 10.18129/B9.bioc.EventPointer  

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

Bioconductor version: Release (3.16)

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 [aut], Juan A. Ferrer-Bonsoms [aut, cre], Pablo Sacristan [aut], Ander Muniategui [aut], Fernando Carazo [aut], Ander Aramburu [aut], Angel Rubio [aut]

Maintainer: Juan A. Ferrer-Bonsoms <jafhernandez at tecnun.es>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	EventPointer
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, DifferentialSplicing, ImmunoOncology, RNASeq, Sequencing, Software, TimeCourse, Transcription, mRNAMicroarray
Version	3.6.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), 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, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra
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_3.6.0.tar.gz
Windows Binary	EventPointer_3.6.0.zip
macOS Binary (x86_64)	EventPointer_3.6.0.tgz
macOS Binary (arm64)	EventPointer_3.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EventPointer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EventPointer
Bioc Package Browser	https://code.bioconductor.org/browse/EventPointer/
Package Short Url	https://bioconductor.org/packages/EventPointer/
Package Downloads Report	Download Stats