MAnorm

Description

manorm website

ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed. Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators. The hdf5 module sets the following environment variables:

Environment Modules

Run module spider manorm to find out what environment modules are available for this application.

Environment Variables

• HPC_MANORM_DIR - main directory
• HPC_MANORM_BIN - executable binary directory

Citation

If you publish research that uses manrom you have to cite it as follows:

Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. (2012) MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biol. Mar 16;13(3):R16.

Categories

biology, phylogenetics