GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)

bigmw

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GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)

04-18-2014, 05:49 PM

Both gage and pathview packages were updated with recently Bioconductor 2.14 release. GAGE/Pathview now support ~ 3000 KEGG species. Function kegg.gsets in gage package is used to generate updated KEGG pathway gene set data.
We also added function go.gsets in gage package, which generates up-to-date GO gene sets for 19 common species annotated in Bioconductor and more others by the users.
Please check the latest release version for these updates:

gage

http://bioconductor.org/packages/release/bioc/html/gage.html

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.

pathview

http://bioconductor.org/packages/release/bioc/html/pathview.html

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
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GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)

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