Package: EventPointer
Type: Package
Title: An effective identification of alternative splicing events using
        junction arrays and RNA-Seq data
Version: 3.0.0
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"),
  person("Ander", "Muniategui"),
  person("Fernando", "Carazo"),
  person("Ander", "Aramburu"),
  person("Angel", "Rubio")
    )
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). 
		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: 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
Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
        kableExtra
License: Artistic-2.0
LazyData: true
RoxygenNote: 7.1.1
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: RELEASE_3_13
git_last_commit: e4f2123
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: yes
Packaged: 2021-05-20 00:00:59 UTC; biocbuild
Author: Juan Pablo Romero [aut],
  Juan A. Ferrer-Bonsoms [aut, cre]
Maintainer: Juan A. Ferrer-Bonsoms <jafhernandez@tecnun.es>
Built: R 4.1.0; i386-w64-mingw32; 2021-05-20 08:02:29 UTC; windows
Archs: i386, x64
