Package: PathwaySplice
Type: Package
Title: An R Package for Unbiased Splicing Pathway Analysis
Version: 1.8.0
Author: Aimin Yan, Xi Chen, Lily Wang
Maintainer: Aimin Yan <aimin.at.work@gmail.com>
Depends: R (>= 3.5.0)
Imports: goseq, Biobase, DOSE, reshape2, igraph, org.Hs.eg.db,
        org.Mm.eg.db, BiocGenerics, AnnotationDbi, JunctionSeq,
        BiasedUrn, GO.db,gdata, geneLenDataBase, grDevices, graphics,
        stats, utils, VennDiagram, RColorBrewer, ensembldb,
        AnnotationHub, S4Vectors, dplyr, plotly, webshot, htmlwidgets ,
        mgcv ,gridExtra, grid ,gplots, tibble , EnrichmentBrowser,
        annotate , KEGGREST
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
biocViews: ImmunoOncology, AlternativeSplicing, DifferentialSplicing,
        GeneSetEnrichment, GO, RNASeq, Sequencing, Software,
        Visualization, NetworkEnrichment, Network, Pathways,
        GraphAndNetwork, Regression
Description: Pathway analysis of alternative splicing would be biased without accounting for the different 
            number of exons associated with each gene, because genes with higher number of exons are more 
            likely to be included in the 'significant' gene list in alternative splicing. 
            PathwaySplice is an R package that: 
              (1) performs pathway analysis that explicitly adjusts for the number of exons 
                  associated with each gene 
              (2) visualizes selection bias due to different number of exons for each gene 
              (3) formally tests for presence of bias using logistic regression 
              (4) supports gene sets based on the Gene Ontology terms, as well as 
                  more broadly defined gene sets (e.g. MSigDB) or user defined gene sets
              (5) identifies the significant genes driving pathway significance 
              (6) organizes significant pathways with an enrichment map, 
                  where pathways with large number of overlapping genes are 
                  grouped together in a network graph
License: LGPL(>=2)
LazyData: TRUE
RoxygenNote: 6.0.1
git_url: https://git.bioconductor.org/packages/PathwaySplice
git_branch: RELEASE_3_9
git_last_commit: 775b448
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02
NeedsCompilation: no
Packaged: 2019-05-03 05:01:07 UTC; biocbuild
Built: R 3.6.0; ; 2019-05-03 14:05:51 UTC; windows
