Signal-level algorithms for MinION data

• UpdatedAug 5, 2023
• C++

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

• UpdatedAug 8, 2025
• HTML

R package for DNA methylation analysis

• UpdatedSep 7, 2025
• R

A bioinformatics tool for working with modified bases

• UpdatedSep 11, 2025
• Rust

Methylation/modified base calling separated from basecalling.

• UpdatedSep 17, 2024
• Python

A (mostly) universal methylation extractor for BS-seq experiments.

• UpdatedJun 21, 2024
• C

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

• UpdatedMay 18, 2025
• Python

Deep neural networks for predicting CpG methylation

• UpdatedSep 30, 2019
• Python

Detecting methylation using signal-level features from Nanopore sequencing reads

• UpdatedJun 4, 2023
• Python

• UpdatedMar 3, 2025
• Python

Arioc: GPU-accelerated DNA short-read alignment

• UpdatedMay 20, 2025

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

• UpdatedJul 1, 2024
• Python

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

• UpdatedMay 9, 2025
• R

CpGPT: a Foundation Model for DNA Methylation.

• UpdatedSep 5, 2025
• Python

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads

• UpdatedMar 5, 2025
• Jupyter Notebook

MethPhaser: methylation-based haplotype phasing of human genomes

• UpdatedMar 5, 2025
• Python

Python package to analyze DNA methylation data

• UpdatedOct 9, 2025
• Python

A battery of methylation tools for PacBio HiFi reads

• UpdatedNov 4, 2025

Python-based preprocessing software for Illumina methylation arrays

• UpdatedAug 17, 2023
• Python

A bioinformatics tool for viewing and calculating base modification frequencies from BAM files

• UpdatedNov 4, 2025
• C