methylKit • Rank 20.8 • Science 46%

R package for DNA methylation analysis

aric • Rank 3.8 • Science 46%

Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

BEclear • Rank 15.3 • Science 23%

Correction of batch effects in DNA methylation data

methylGSA • Rank 14.0 • Science 23%

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing

https://github.com/shitohana/BSXplorer • Rank 6.9 • Science 26%

Comprehensive tool for visualizing genome-wide cytosine data.

scmeth • Science 10%

Shiny-WGCNA • Science 49%

Shiny app for WGCNA for RNAseq and DNA methylation data