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Epigenetics Python Packages

Python packages with the GitHub topic epigenetics. Sorted by relevance, with stars and monthly downloads.
FOXOBioScience
methylprep

Python-based preprocessing software for Illumina methylation arrays

4K 42 16
brj0
mepylome

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

2K 10 1
eliopato
pylluminator

Python package for processing and analyzing Illumina DNA methylation data

1K 11 1
liguowang
cpgtools

Python package to analyze DNA methylation data

767 45 13
nanoporetech
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.

750 204 27
fraenkel-lab
garnet

No description available

740 4 2
BIMSBbioinfo
janggu

Utilities and datasets for deep learning in genomics

680 258 35
Genome-Function-Initiative-Oxford
zen-norm

Zone Equalisation Normalisation: A Python package for bigWig scaling

551 1 0
andrewdavidsmith
pyxfr

The Transferase Python API

519 4 0
KarrLab
bpforms

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

513 7 2
cangermueller
deepcpg

Deep neural networks for predicting CpG methylation

468 152 71
aryeelab
hichipper

A preprocessing and QC pipeline for HiChIP data

446 40 15
caleblareau
mgatk

Mitochondrial genome analysis toolkit.

395 111 29
MuteJester
pyncbi

A Python API library for exploration and data retrieval from NCBI

328 3 3
nanoporetech
ont-tombo

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

323 233 54
bioinfomaticsCSU
deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

314 118 23
ChaorongC
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.

302 2 0
caleblareau
bap-atac

Bead-based single-cell atac processing

162 33 8
eliopato
pylluminator-modern

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

92 11 1
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