Methylation Python Packages

methylprep

Python-based preprocessing software for Illumina methylation arrays

bsbolt

BiSulfite Bolt - A Bisulfite Sequencing Alignment and Processing Tool

bam2tensor

Convert methylation data to sparse objects for machine learning.

cpgpt

CpGPT: a Foundation Model for DNA Methylation.

mepylome

Python package for processing Infinum DNA methylation arrays

cemba-data

Pipelines for single nucleus methylome and multi-omic dataset.

methylgrapher

Methylation analysis pipeline for genome graph

methylize

EWAS Analysis software for Illumina methylation arrays

cpgtools

Tools to analyze and visualize DNA methylation data

bsxplorer

Analytical framework for BS-seq data comparison and visualization

bismarkplot

Analytical framework for BS-seq data comparison and visualization

ont-remora

Methylation/modified base calling separated from basecalling.

bpforms

Unambiguous representation of modified DNA, RNA, and proteins

pyllelic

pyllelic: a tool for detection of allele-specific methylation variation in bisulfite DNA sequencing.

methscan

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

deepcpg

Deep neural networks for predicting CpG methylation

pyncbi

A Python API library for exploration and data retrieval from NCBI

methurator

Methurator is a Python package designed to estimate CpGs saturation for DNA methylation sequencing data.

pyxfr

The Transferase Python API

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

hmmcdr

Accurately find CDRs and boundaries using a Hidden Markov Model

mesa-cfdna

A flexible and sensitive method for capturing and integrating multimodal epigenetic information from cell-free DNA (cfDNA) using a single experimental assay.

deepsignal-plant

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

methylink

CLI tool to link methylation tags between two files