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
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-12-04 08:57:09 UTC
RemoteUrl: https://github.com/bioc/EventPointer
RemoteRef: HEAD
RemoteSha: 08861cc5e848d8293eef6e24b3fc3d237c52d2c5
NeedsCompilation: yes
Packaged: 2025-12-05 03:28:07 UTC; root
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>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-12-05 03:31:01 UTC; windows
Archs: x64
