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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | |
| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/EventPointer/ |
| Package Short Url | https://bioconductor.org/packages/EventPointer/ |
| Package Downloads Report | Download Stats |