Package: EventPointer Type: Package Title: An effective identification of alternative splicing events using junction arrays and RNA-Seq data Version: 3.15.0 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). 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, 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