EventPointer
This is the released version of EventPointer; for the devel version, see EventPointer.
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
Bioconductor version: Release (3.23)
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). In the latter, EventPointer can work with annotated splicing events or can build a splicing graph from the RNA-Seq reads and then identify new and specific alternative splicing events. 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("EventPointer")):Juan Pablo Romero, Juan A. Ferrer-Bonsoms, Pablo Sacristan, Ander Muniategui, Fernando Carazo, Ander Aramburu, Angel Rubio. EventPointer: An effective identification of alternative splicing events using junction arrays and RNA-Seq data. doi:10.18129/B9.bioc.EventPointer, R package version 3.20.0, https://bioconductor.org/packages/EventPointer.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, DifferentialSplicing, ImmunoOncology, RNASeq, Sequencing, Software, TimeCourse, Transcription, mRNAMicroarray |
| Version | 3.20.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment |
| Imports | txdbmaker, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, GenomicAlignments, Rsamtools, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, aroma.light, iterators, lpSolve, poibin, speedglm, tximport, fgsea |
| 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 | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EventPointer_3.20.0.tar.gz |
| Windows Binary (x86_64) | EventPointer_3.20.0.zip |
| macOS Binary (big-sur-x86_64) | EventPointer_3.20.0.tgz |
| macOS Binary (sonoma-arm64) | EventPointer_3.20.0.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 | https://bioconductor.org/packages/EventPointer/ |
| Package Downloads Report | Download Stats |