甲基化相关文章的code

文献名：Spatiotemporal DNA methylome dynamics of the developing mouse fetus
代码：
https://github.com/yupenghe/methylpy
https://github.com/yupenghe/encode_dna_dynamics

从公众号剪藏了一篇解读这篇文章的推文，如果对文章感兴趣可以去看一看。
Nature | 小鼠胚胎发育过程中的DNA甲基化时空动态变化

摘抄出文章的方法部分，如何表述甲基化水平：
Calculation of methylation level
Methylation level was computed to measure the intensity and degree of DNA methylation of single cytosines or larger genomic regions. The methylation level is defined as the ratio of the sum of methylated basecall counts over the sum of both methylated and unmethylated basecall counts at one cytosine or across sites in a given region53, subtracting the sodium bisulfite non-conversion rate. The sodium bisulfite non-conversion rate is defined as the methylation level of the bisulfite-treated lambda genome.
We calculated this metric for cytosines in both CG context and CH contexts (H = A, C or T). The former is called the CG methylation (mCG) level or mCG level and the latter is called the CH methylation (mCH) level or mCH level.