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- AtlasRDF
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("AtlasRDF")
In most cases, you don't need to download the package archive at all.
AtlasRDF
Gene Expression Atlas query and gene set enrichment package.
Bioconductor version: 2.14
Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.
Author: James Malone, Simon Jupp, Maryam Soleimani
Maintainer: James Malone <malone at ebi.ac.uk>
Citation (from within R,
enter citation("AtlasRDF")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("AtlasRDF")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("AtlasRDF")
| R Script | An introduction to the AtlasRDF-R package | |
| Reference Manual |
Details
| biocViews | DataImport, DataRepresentation, DifferentialExpression, GeneExpression, GeneSetEnrichment, Microarray, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | Apache License 2.0 |
| Depends | R (>= 2.10), hash, SPARQL, methods |
| Imports | |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | AtlasRDF_1.0.0.tar.gz |
| Windows Binary | AtlasRDF_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | AtlasRDF_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | AtlasRDF_1.0.0.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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