Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts

rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments

SUMMARY Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) has evolved as a popular technique to study DNA-protein binding or post-translational chromatin/histone modifications at the genomic level. However, the raw microarray intensities generate a massive amount of data, creating a need for efficient analysis algorithms and statistical methods to identify enriched regions...

An integrated software system for analyzing ChIP - chip and ChIP - seq data ( Supplementary Information )

ChIP-chip and ChIP-seq are powerful technologies to study transcriptional regulation in complex genomes, however, mining information from the huge datasets generated by these highthroughput technologies remains to be a non-trivial task. To analyze a ChIP-chip experiment, one usually starts with data exploration and then goes through normalization, binding region detection, adding gene annotatio...

CAD Flows for Chip - Package

A unified method is presented for layout and package design implemented within a commercial design environment that will reduce design time and enable chip-package codesign.

Analyzing ChIP-chip Data Using Bioconductor

The interpretation of ChIP-chip data poses two computational challenges: first, what can be termed primary statistical analysis, which includes quality assessment, data normalization and transformation, and the calling of regions of interest; second, integrative bioinformatic analysis, which interprets the data in the context of existing genome annotation and of related experimental results obt...

Supplement: Analyzing ChIP-chip data using Bioconductor