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News: Announcing the EnrichmentBrowser 2.0
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gravatar for Ludwig Geistlinger
2.7 years ago by
USA/NYC/CUNY
Ludwig Geistlinger40 wrote:
Dear Bioconductors,

I am delighted to announce a major re-release of the EnrichmentBrowser
package in line with its recent publication:

Geistlinger L, Csaba G, Zimmer R.
Bioconductor's EnrichmentBrowser: seamless navigation through combined
results of set- & network-based enrichment analysis.
BMC Bioinformatics, 17:45, Jan 2016.
http://doi.org/10.1186/s12859-016-0884-1


The EnrichmentBrowser is a meta-package implementing an analysis pipeline
for high-throughput gene expression data as measured with microarrays and
RNA-seq.
Functionality includes data preparation, preprocessing, differential
expression analysis, set- and network-based enrichment analysis,
combination as well as visualization and exploration of results.
In a workflow-like manner, the package brings together a selection of
finest Bioc packages which have shown to work distinghuishably well in
practice for the respective purposes.
Additional features of the package are the adaption of enrichment methods
using sample permutation for RNA-seq read count data, an improved
implementation of the network-based enrichment method GGEA (Geistlinger et
al., Bioinformatics, ISMB/ECCB 2011), and novel ways of combining and
exploring results across methods.

Comments and suggestions to further improve the EnrichmentBrowser are
highly appreciated.

 
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