PathwaySplice

DOI: 10.18129/B9.bioc.PathwaySplice    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

An R Package for Unbiased Splicing Pathway Analysis

Bioconductor version: Release (3.12)

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

Author: Aimin Yan, Xi Chen, Lily Wang

Maintainer: Aimin Yan <aimin.at.work at gmail.com>

Citation (from within R, enter citation("PathwaySplice")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PathwaySplice")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews AlternativeSplicing, DifferentialSplicing, GO, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Regression, Sequencing, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.6 (R-3.4) (3 years)
License LGPL(>=2)
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
LinkingTo
Suggests testthat, knitr, rmarkdown
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/PathwaySplice
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PathwaySplice
Package Short Url https://bioconductor.org/packages/PathwaySplice/
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