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>
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")| PAST | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneSetEnrichment, Pathways, Software |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | GPL (>=3) |
| Depends | R (>= 3.6) |
| Imports | stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2 |
| 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.
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/PAST/ |
| Package Short Url | https://bioconductor.org/packages/PAST/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |