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Bioconductor - PAST

PAST

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see PAST.

Pathway Association Study Tool (PAST)

Bioconductor version: 3.10

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 "3.6") 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")
Details biocViews GeneSetEnrichment, Pathways, Software Version 1.2.8 In Bioconductor since BioC 3.9 (R-3.6) (5 years) License GPL (>=3) + file LICENSE Depends R (>= 3.6) Imports stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors System Requirements URL https://github.com/IGBB/past Bug Reports https://github.com/IGBB/past/issues See More Suggests knitr, rmarkdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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