PAST

DOI: 10.18129/B9.bioc.PAST    

Pathway Association Study Tool (PAST)

Bioconductor version: Release (3.9)

PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.

Author: Thrash Adam [aut, cre], DeOrnellis Mason [aut]

Maintainer: Thrash Adam <thrash at igbb.msstate.edu>

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

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("PAST")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("PAST")

 

HTML R Script PAST
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GeneSetEnrichment, Pathways, Software
Version 1.0.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License GPL (>=3)
Depends R (>= 3.6)
Imports stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2
LinkingTo
Suggests knitr, rmarkdown
SystemRequirements
Enhances
URL https://github.com/IGBB/past
BugReports https://github.com/IGBB/past/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package PAST_1.0.0.tar.gz
Windows Binary PAST_1.0.0.zip
Mac OS X 10.11 (El Capitan) PAST_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PAST
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PAST
Package Short Url http://bioconductor.org/packages/PAST/
Package Downloads Report Download Stats

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