PAST

This is the development version of PAST; for the stable release version, see PAST.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

Pathway Association Study Tool (PAST)

Bioconductor version: Development (3.24)

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")):

Thrash Adam, DeOrnellis Mason. PAST: Pathway Association Study Tool (PAST). doi:10.18129/B9.bioc.PAST, R package version 1.29.0, https://bioconductor.org/packages/PAST.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneSetEnrichment, Pathways, Software
Version	1.29.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	GPL (>=3) + file LICENSE
Depends	R (>= 4.0)
Imports	stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors
System Requirements
URL	https://github.com/IGBB/past
Bug Reports	https://github.com/IGBB/past/issues

Suggests	knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	PAST_1.29.0.tar.gz
Windows Binary (x86_64)	PAST_1.29.0.zip
macOS Binary (big-sur-x86_64)	PAST_1.29.0.tgz
macOS Binary (sonoma-arm64)	PAST_1.29.0.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	https://bioconductor.org/packages/PAST/
Package Downloads Report	Download Stats