10.7 Other R packages that can be used for methylation analysis

• DSS beta-binomial models with empirical Bayes for moderating dispersion.
• BSseq Regional differential methylation analysis using smoothing and linear-regression-based tests.
• BiSeq Regional differential methylation analysis using beta-binomial models.
• MethylSeekR: Methylome segmentation using HMM and cutoffs.
• QuasR: Methylation aware alignment and methylation calling, as well as fastQC-like fastq raw data quality check features.