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

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.

zen-norm

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

garnet

No description available

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.

janggu

Deep learning infrastructure for genomics

pylluminator

Python package for processing and analyzing Illumina DNA methylation data

diffmethyltools

A pipeline for detecting, visualizing and annotating Differentially Methylated Loci and Regions

deepcpg

Deep neural networks for predicting CpG methylation

mgatk

Mitochondrial genome analysis toolkit.

pyxfr

The Transferase Python API

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

Simple API for Python Integration with NCBI GEO Database

bap-atac

Bead-based single-cell atac processing

pylluminator-modern

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

stackimpute

Deep neural networks for predicting CpG methylation