Epigenetics 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

cpgtools

Python package to analyze DNA methylation data

megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

garnet

No description available

janggu

Deep learning infrastructure for genomics

pyxfr

The transferase system for retrieving methylome data from methbase

bpforms

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

mesa-cfdna

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

diffmethyltools

An automated, end-to-end Python pipeline for differential DNA methylation analysis, region annotation, and visualization.

pylluminator

Python package for processing and analyzing Illumina DNA methylation data

mgatk

mgatk: mitochondrial genome analysis toolkit

zen-norm

ZEN-norm is a Python package for normalising bigWigs of genomic signal, reversing prior normalisation and benchmarking normalisation method performance.

hichipper

A preprocessing and QC pipeline for HiChIP data

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

ont-tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

pyncbi

A Python API library for exploration and data retrieval from NCBI

deepcpg

Deep neural networks for predicting CpG methylation

bap-atac

Bead-based single-cell atac processing

pylluminator-modern

Python package for processing and analyzing Illumina DNA methylation data

stablednam

StableDNAm: stable and efficient DNA methylation prediction with adaptive feature correction learning (BMC Genomics, 2023)

stackimpute

Deep neural networks for predicting CpG methylation