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- ReactomePA
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ReactomePA")
In most cases, you don't need to download the package archive at all.
ReactomePA
Reactome Pathway Analysis
Bioconductor version: 2.14
This package provides functions for pathway analysis based on REACTOME pathway database. It will implement enrichment analysis, gene set enrichment analysis and functional modules detection.
Author: Guangchuang Yu <guangchuangyu at gmail.com>
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
Citation (from within R,
enter citation("ReactomePA")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ReactomePA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ReactomePA")
| R Script | ReactomePA - an R package for Reactome Pathway Analysis | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, Pathways, Software, Visualization |
| Version | 1.8.1 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL-2 |
| Depends | |
| Imports | AnnotationDbi, reactome.db, org.Hs.eg.db, DOSE, igraph, graphite |
| Suggests | clusterProfiler, GOSemSim, ChIPseeker, knitr |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | ChIPseeker, clusterProfiler, DOSE |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ReactomePA_1.8.1.tar.gz |
| Windows Binary | ReactomePA_1.8.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ReactomePA_1.8.1.tgz |
| Mac OS X 10.9 (Mavericks) | ReactomePA_1.8.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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