Methylation/modified base calling separated from basecalling.

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

Deep neural networks for predicting CpG methylation

Detecting methylation using signal-level features from Nanopore sequencing reads

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

CpGPT: a Foundation Model for DNA Methylation.

MethPhaser: methylation-based haplotype phasing of human genomes

Python package to analyze DNA methylation data

Python-based preprocessing software for Illumina methylation arrays

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

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

BiSulfite Bolt - A Bisulfite Sequencing Alignment and Processing Tool

Mapping pipeline for snmC-seq based technologies.

Python package with CLI for the analysis of single cell methylation data.

Methylation analysis pipeline for genome graph

Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files

Comprehensive tool for visualizing genome-wide cytosine data.

An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq samples, including cfDNA.

A comprehensive DNA methylation atlas for the Chinese population through nanopore long-read sequencing of 106 individuals