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

pylluminator

Python package for processing and analyzing Illumina DNA methylation data

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

Utilities and datasets for deep learning in genomics

zen-norm

Zone Equalisation Normalisation: A Python package for bigWig scaling

pyxfr

The Transferase Python API

bpforms

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

deepcpg

Deep neural networks for predicting CpG methylation

hichipper

A preprocessing and QC pipeline for HiChIP data

mgatk

Mitochondrial genome analysis toolkit.

pyncbi

A Python API library for exploration and data retrieval from NCBI

ont-tombo

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

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.

bap-atac

Bead-based single-cell atac processing

pylluminator-modern

Tool to preprocess, analyze and visualize DNA methylation data from Illumina micro-arrays