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PAST

Pathway Association Study Tool (PAST)

Bioconductor version: Release (3.17)

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 [cre, aut], 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 "4.3") and enter: 

if (!require("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")
PAST HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneSetEnrichment, Pathways, Software
Version 1.16.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License GPL (>=3) + file LICENSE
Depends R (>= 4.0)
Imports stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors
Linking To
Suggests knitr, rmarkdown
System Requirements
Enhances
URL https://github.com/IGBB/past
Bug Reports https://github.com/IGBB/past/issues
See More
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_1.16.0.tar.gz
Windows Binary PAST_1.16.0.zip
macOS Binary (x86_64) PAST_1.16.0.tgz
macOS Binary (arm64) PAST_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PAST
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PAST
Bioc Package Browser https://code.bioconductor.org/browse/PAST/
Package Short Url https://bioconductor.org/packages/PAST/
Package Downloads Report Download Stats