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The MeDiChI Model-Based ChIP-chip Deconvolution Algorithm

MeDiChI R package

This is the download and instruction page for the MeDiChI software in support of the Bioinformatics manuscript
"Model-based deconvolution of genome-wide DNA binding",
by David J Reiss, Marc T Facciotti, and Nitin S Baliga.

Please cite this publication if you utilize this package for your published research.

MeDiChI is method for the automated, model-based deconvolution of protein-DNA binding (Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray -- ChIP-chip) data that discovers DNA binding sites at high resolution (higher resolution than that of the tiling array itself). This enables more stringent analysis of the functional binding (including regulated genes and DNA binding motifs), than would be possible using standard procedures for enrichment detection. The procedure uses a generative model of protein-DNA binding sites, and a linear model of the cumulative effect of those sites on the intensity of microarray probes. It uses constrained linear regression and L1 shrinkage to estimate the parameters of the linear model, which correspond to the high-resolution locations and intensities of the binding peaks. Finally a bootstrap is used to estimate the uncertainties and significance of each binding site.

We have developed a MeDiChI R package (including all functions for analysis and visualization, and all novel data presented in the manuscript).

Please visit our Github repository for downloads, source code, installation instructions, and basic usage.