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EventPointer

This is the development version of EventPointer; for the stable release version, see EventPointer.

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

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 3.9.0
In Bioconductor since BioC 3.5 (R-3.4) (6.5 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
Linking To
Suggests knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra
System Requirements
Enhances
URL
Bug Reports https://github.com/jpromeror/EventPointer/issues
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Package Archives

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

Source Package EventPointer_3.9.0.tar.gz
Windows Binary EventPointer_3.9.0.zip
macOS Binary (x86_64) EventPointer_3.9.0.tgz
macOS Binary (arm64) EventPointer_3.9.0.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