rMAT--一个用于分析 ChIP-chip 实验的 R/Bioconductor 包。
rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.
机构信息
Institut de recherches cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada.
出版信息
Bioinformatics. 2010 Mar 1;26(5):678-9. doi: 10.1093/bioinformatics/btq023. Epub 2010 Jan 19.
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.
RESULTS
We present a fast, free and powerful, open source R package, rMAT, that allows the identification of regions enriched for transcription factor binding sites in ChIP-chip experiments on Affymetrix tiling arrays.
AVAILABILITY
The R-package rMAT is available from the Bioconductor web site at http://bioconductor.org and runs on Linux, MAC OS and MS-Windows. rMAT is distributed under the terms of the Artistic Licence 2.0.
摘要
染色质免疫沉淀结合 DNA 微阵列（ChIP-chip）已发展成为一种研究基因组水平 DNA-蛋白质结合或翻译后染色质/组蛋白修饰的流行技术。然而，原始的微阵列强度产生了大量的数据，需要有效的分析算法和统计方法来识别富集区域。
结果
我们提出了一个快速、免费且功能强大的开源 R 包 rMAT，它允许在 Affymetrix 平铺阵列的 ChIP-chip 实验中识别转录因子结合位点富集的区域。
可用性
R 包 rMAT 可从 Bioconductor 网站获得，网址为 http://bioconductor.org，可在 Linux、MAC OS 和 MS-Windows 上运行。rMAT 根据 Artistic Licence 2.0 分发。
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