Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
☄️ Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
Toolkit for single-cell DNA methylation analysis.
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)
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
Nanomotif - a tool for identifying methylated motifs in metagenomic samples
Modelling DNA methylation profiles
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)
R package for DNA methylation analysis
A chronological age predictor based on DNA methylation
TFregulomeR reveals transcription factors’ context-specific features and functions
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