Methylation Python Packages

methylprep

Python-based preprocessing software for Illumina methylation arrays

16K 42 16

mepylome

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

3K 11 1

bpforms

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

2K 7 2

bsbolt

BiSulfite Bolt - A Bisulfite Sequencing Alignment and Processing Tool

2K 26 10

methylize

Python-based Illumina methylation array analysis software

1K 16 7

cpgpt

CpGPT: A Foundation Model for DNA Methylation

1K 76 15

bam2tensor

Convert methylation data to sparse objects for machine learning.

1K 1 0

ont-remora

Methylation/modified base calling separated from basecalling.

1K 188 28

cemba-data

Mapping pipeline for snmC-seq based technologies.

915 20 9

modulector-sdk

An open platform which provides information about miRNAs and genes from different popular databases

858 5 0

mesa-cfdna

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

846 3 1

cpgtools

Python package to analyze DNA methylation data

722 45 12

methurator

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

606 1 1

bsxplorer

Comprehensive tool for visualizing genome-wide cytosine data.

524 8 0

deepsignal-plant

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

520 67 10

bismarkplot

Comprehensive tool for visualizing genome-wide cytosine data.

500 8 0

pyllelic

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

460 6 2

hmmcdr

Find CDR locations using bedmethyl file and CenSat annotations. (REQUIRES BEDTOOLS INSTALLED)

426 1 0

deepcpg

Deep neural networks for predicting CpG methylation

402 153 71

methscan

a command line tool for Single-Cell Analysis of Methylation data

379 20 7

pyxfr

The Transferase Python API

374 4 0

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

331 120 23

pyncbi

Simple API for Python Integration with NCBI GEO Database

277 3 3

modulector

An open platform which provides information about miRNAs and genes from different popular databases

248 5 0