BELT (Bin-based Enrichment Level Threshold) is a ChIP-seq peak calling tool. This is the engine used in our published web application W-ChIPeaks, meant to be used as a command-line application. Although it does not include all of the features of W-ChIPeaks (such as archive support and target FDR) as some of these are implemented by the Web-based framework, it is nonetheless a full-fledged standalone peakcalling utility.
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Bioinformatics. 2011 Feb 1;27(3):428-30. doi: 10.1093/bioinformatics/btq669. Epub 2010 Dec 7.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Lan X1, Bonneville R, Apostolos J, Wu W, Jin VX.