Package: EventPointer
Type: Package
Title: An effective identification of alternative splicing events using
        junction arrays and RNA-Seq data
Version: 3.19.0
Authors@R: c(person("Juan Pablo","Romero",role=c("aut"),email = "jpromero@ceit.es"),
  person("Juan A.", "Ferrer-Bonsoms",role=c("aut","cre"),email = "jafhernandez@tecnun.es"),
  person("Pablo", "Sacristan",role=c("aut"),email = "a904719@alumni.unav.es"),
  person("Ander", "Muniategui",role=c("aut")),
  person("Fernando", "Carazo",role=c("aut")),
  person("Ander", "Aramburu",role=c("aut")),
  person("Angel", "Rubio",role=c("aut"),email = "arubio@tecnun.es")
    )
Description: 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.
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, S4Vectors,
        IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet,
        abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea
Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
        kableExtra
License: Artistic-2.0
LazyData: true
RoxygenNote: 7.1.2
Encoding: UTF-8
biocViews: AlternativeSplicing, DifferentialSplicing, mRNAMicroarray,
        RNASeq, Transcription, Sequencing, TimeCourse, ImmunoOncology
VignetteBuilder: knitr
Url: https://github.com/jpromeror/EventPointer
BugReports: https://github.com/jpromeror/EventPointer/issues
git_url: https://git.bioconductor.org/packages/EventPointer
git_branch: devel
git_last_commit: b184430
git_last_commit_date: 2025-12-03
Repository: Bioconductor 3.23
Date/Publication: 2025-12-03
NeedsCompilation: yes
Packaged: 2025-12-03 22:46:53 UTC; biocbuild
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@tecnun.es>
