methylation

Signal-level algorithms for MinION data

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

A bioinformatics tool for working with modified bases

R package for DNA methylation analysis

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

Methylation/modified base calling separated from basecalling.

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

Deep neural networks for predicting CpG methylation

Detecting methylation using signal-level features from Nanopore sequencing reads

DeepCatch: performance-weighted multi-modal fusion for ultra-early cfDNA cancer detection. Fragmentomics, methylation, sequence.

CpGPT: a Foundation Model for DNA Methylation.

Arioc: GPU-accelerated DNA short-read alignment

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

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

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

A battery of methylation tools for PacBio HiFi reads

MethPhaser: methylation-based haplotype phasing of human genomes

Python package to analyze DNA methylation data

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