1、支持分析Illumina Infinium HumanMethylation450 BeadChip

2、计算性能高：分析速度快、占用内存少、支持多核多进程

3、多种差异DNA甲基化分析模式：单位点分析、预设区域分析、全基因组区域分析

4、提供多种注释：CpGi、基因、miRNA等

软件免费下载地址 http://bioinfo.au.tsinghua.edu.cn/software/fastdma

FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer

DNA methylation is vital for many essential biological processes and human diseases. Illumina Infinium HumanMethylation450 Beadchip is a recently developed platform studying genome-wide DNA methylation state on more than 480,000 CpG sites and a few CHG sites with high data quality. To analyze the data of this promising platform, we developed FastDMA which can be used to identify significantly differentially methylated probes. Besides single probe analysis, FastDMA can also do region-based analysis for identifying the differentially methylated region (DMRs). A uniformed statistical model, analysis of covariance (ANCOVA), is used to achieve all the analyses in FastDMA. We apply FastDMA on three large-scale DNA methylation datasets from The Cancer Genome Atlas (TCGA) and finds many differentially methylated genomic sites in different types of cancer. On the testing datasets, FastDMA shows much higher computational efficiency than current tools. FastDMA can benefit the data analyses of large-scale DNA methylation studies with an integrative pipeline and a high computational efficiency. The software is freely available via http://bioinfo.au.tsinghua.edu.cn/software/fastdma/.
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