Package: EventPointer
Type: Package
Title: An effective identification of alternative splicing events using
        junction arrays and RNA-Seq data
Version: 2.2.4
Author: Juan Pablo Romero, Juan A. Ferrer-Bonsoms, Pablo Sacristan, Ander Muniategui, Fernando Carazo, Ander Aramburu, Angel Rubio
Maintainer: Juan Pablo Romero <jpromero@ceit.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). 
		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 (>= 3.4), 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,
        BSgenome.Hsapiens.UCSC.hg38, Biostrings
Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
        kableExtra
License: Artistic-2.0
LazyData: true
RoxygenNote: 6.1.0
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_9
git_last_commit: ff24eb8
git_last_commit_date: 2019-06-03
Date/Publication: 2019-06-03
NeedsCompilation: no
Packaged: 2019-06-04 02:06:54 UTC; biocbuild
Built: R 3.6.1; ; 2019-08-13 07:54:27 UTC; unix
