AMEN stands for Annotation, Mapping, Expression and Network and is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.
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Requirements:
· Tcl/Tk
What's New in This Release: [ read full changelog ]
7 modules:
· Module to estimate if a biological entity (protein for exemple) interacts or regulates more genes/proteins in a cluster of genes as compared to whole genes (Enrichment on regulatory or interaction networks). Written by Aurélie Lardenois.
· Module to visualize these enrichments as a network. Written by Aurélie Lardenois.
· Two modules for semi-supervised k-means and PAM methods.
· Module to add gene set files (.gmt files from GSEA) into the annotation file.
· Module to normalize with positive or negative control genes.
· Module to reorganize the samples into an expression file
Two changes:
· When importing group files they are now sorted in the alphabetical order and then imported into AMEN
· The R packages installation module was modified.
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