Methylation Python Packages

methylprep

Python-based preprocessing software for Illumina methylation arrays

mepylome

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

bsbolt

Bisulfite Sequencing Processing Platform

bam2tensor

Convert methylation data to sparse objects for machine learning.

cemba-data

Mapping pipeline for snmC-seq based technologies.

pyllelic

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

cpgpt

CpGPT: a Foundation Model for DNA Methylation.

bsxplorer

Analytical framework for BS-seq data comparison and visualization

methylize

Python-based Illumina methylation array analysis software

cpgtools

Python package to analyze DNA methylation data

ont-remora

Methylation/modified base calling separated from basecalling.

bismarkplot

Comprehensive tool for visualizing genome-wide cytosine data.

pyxfr

The Transferase Python API

bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

deepcpg

Deep neural networks for predicting CpG methylation

methurator

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

methscan

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

hmmcdr

Accurately find CDRs and boundaries using a Hidden Markov Model

pyncbi

A Python API library for exploration and data retrieval from NCBI

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

mesa-cfdna

Multimodal Epigenetic Sequencing Analysis (MESA) is a flexible and sensitive method of capturing and integrating multimodal epigenetic information of cfDNA using a single experimental assay.

methylink

CLI tool to link methylation tags between two files

deepsignal-plant

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

methylgrapher

WGBS data analysis for genome graph