-
recipe
bioconductor-gage¶ GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.
- Homepage
- License
GPL (>=2.0)
- Recipe
- Links
biotools: gage
-
package
bioconductor-gage¶ 
- Versions
2.32.0-0, 2.30.0-0, 2.28.0-0, 2.26.3-0, 2.21.1-0
- Depends bioconductor-annotationdbi
>=1.44.0,<1.45.0
- Depends bioconductor-graph
>=1.60.0,<1.61.0
- Depends bioconductor-keggrest
>=1.22.0,<1.23.0
- Depends r-base
>=3.5.1,<3.5.2.0a0
- Requirements
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-gage
and update with:
conda update bioconductor-gage
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-gage:<tag>
(see bioconductor-gage/tags for valid values for
<tag>)
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-gage/README.html)