Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data

DNA methylation analysis notes from Ming Tang

BISulfite-seq CUI Toolkit

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips

☄️ Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

Toolkit for single-cell DNA methylation analysis.

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.

An R 📦 for fast and flexible DNA methylation analysis

NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)

Predicting regulatory DNA elements based on epigenomic signatures

A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)

Modelling DNA methylation profiles

R package for DNA methylation analysis

A chronological age predictor based on DNA methylation

TFregulomeR reveals transcription factors’ context-specific features and functions

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data