recipe bioconductor-pathwaysplice

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

Homepage

https://bioconductor.org/packages/3.9/bioc/html/PathwaySplice.html

License

LGPL(>=2)

Recipe

/bioconductor-pathwaysplice/meta.yaml

package bioconductor-pathwaysplice

(downloads) docker_bioconductor-pathwaysplice

Versions

1.6.0-0

Depends bioconductor-annotate

>=1.60.0,<1.61.0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-annotationhub

>=2.14.0,<2.15.0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-dose

>=3.8.0,<3.9.0

Depends bioconductor-enrichmentbrowser

>=2.12.0,<2.13.0

Depends bioconductor-ensembldb

>=2.6.0,<2.7.0

Depends bioconductor-genelendatabase

>=1.18.0,<1.19.0

Depends bioconductor-go.db

>=3.7.0,<3.8.0

Depends bioconductor-goseq

>=1.34.0,<1.35.0

Depends bioconductor-junctionseq

>=1.12.0,<1.13.0

Depends bioconductor-keggrest

>=1.22.0,<1.23.0

Depends bioconductor-org.hs.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-org.mm.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-biasedurn

Depends r-dplyr

Depends r-gdata

Depends r-gplots

Depends r-gridextra

Depends r-htmlwidgets

Depends r-igraph

Depends r-mgcv

Depends r-plotly

Depends r-rcolorbrewer

Depends r-reshape2

Depends r-tibble

Depends r-venndiagram

Depends r-webshot

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-pathwaysplice

and update with:

conda update bioconductor-pathwaysplice

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-pathwaysplice:<tag>

(see bioconductor-pathwaysplice/tags for valid values for <tag>)