Do you have recommendations for frameworks or programs for integrating ChIP-seq and RNA-seq or microarray data?
BETA (Binding and Expression Target Analysis) from Cistrome can be utilized for integrating expression data from RNA-seq with ChIP-seq data, specifically transcription factor ChIP-seq data [http://cistrome.org/BETA/]. BETA has three functions:(a) to predict whether the factor has activating or repressive function, (b) to infer the factor’s target genes, and (c) to identify the motif of the factor and its collaborators which might modulate the factor’s activating or repressive function. – by Tovah Markowitz, Paul Schaughency, Vishal Koparde.
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