EventPointer

This package is for version 3.10 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: 3.10

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 A. Ferrer-Bonsoms, Pablo Sacristan, 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 "3.6") 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, ImmunoOncology, RNASeq, Sequencing, Software, TimeCourse, Transcription, mRNAMicroarray
Version 2.4.0
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, IRanges, qvalue, cobs, rhdf5, BSgenome, BSgenome.Hsapiens.UCSC.hg38, Biostrings
System Requirements
URL
Bug Reports https://github.com/jpromeror/EventPointer/issues
See More
Suggests knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package EventPointer_2.4.0.tar.gz
Windows Binary EventPointer_2.4.0.zip
Mac OS X 10.11 (El Capitan) EventPointer_2.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/EventPointer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EventPointer
Bioc Package Browser https://code.bioconductor.org/browse/EventPointer/
Package Short Url https://bioconductor.org/packages/EventPointer/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive