EventPointer

This package is for version 3.18 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: 3.18

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, DifferentialSplicing, ImmunoOncology, RNASeq, Sequencing, Software, TimeCourse, Transcription, mRNAMicroarray

Version 3.10.0

In Bioconductor since BioC 3.5 (R-3.4) (7 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

System Requirements

URL

Bug Reports https://github.com/jpromeror/EventPointer/issues

Suggests knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra

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