BS-seq常用的下游分析软件有

  • methylKit包
  • DSS包
  • CGmaptools
  • viewBS
  • deeptools
  • BatMeth2
  • RnBeads
  • ….

DMR/DMC的基因组注释和富集分析

以下三个工具基本能满足这个需求
Homer
http://homer.ucsd.edu/homer/index.html

ChIPseeker
ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization
https://github.com/YuLab-SMU/ChIPseeker

clusterProfiler
Biomedical Knowledge Mining using GOSemSim and clusterProfiler
https://github.com/YuLab-SMU/clusterProfiler
https://guangchuangyu.github.io/software/ChIPseeker/documentation/

有空把印象笔记的代码搬过来，以前都记录在印象笔记上了