PAST

DOI: 10.18129/B9.bioc.PAST    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PAST.

Pathway Association Study Tool (PAST)

Bioconductor version: 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>

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	1.0.1
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_1.0.1.tar.gz
Windows Binary	PAST_1.0.1.zip
Mac OS X 10.11 (El Capitan)	PAST_1.0.1.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	https://bioconductor.org/packages/PAST/
Package Downloads Report	Download Stats