epigenomics

nf-core/methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

quadbio/Pando

Multiome GRN inference.

Novartis/peax

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

pinellolab/haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

dohlee/metheor

:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

meuleman/epilogos

Methods for summarizing and visualizing multi-biosample functional genomic annotations

lhqing/ALLCools

Toolkit for single-cell DNA methylation analysis.

liguowang/cpgtools

Python package to analyze DNA methylation data

dohlee/chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

caleblareau/bap

Bead-based single-cell atac processing

yupenghe/REPTILE

Predicting regulatory DNA elements based on epigenomic signatures

cantinilab/HuMMuS

Molecular interactions inference from single-cell multi-omics data

broadinstitute/genepy

Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python

itsvenu/ALPS

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

eblancoga/seqcode

Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data

epifluidlab/FinaleToolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

SchulzLab/EpigenomicsTutorial-ISMB2017

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

transbioZI/BioMM

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

vallotlab/ChromSCape

ChromSCape

hoffmangroup/segway

Application for semi-automated genomic annotation.

ma-compbio/GAGE-seq

Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq

ZhangGroup-MITChemistry/DRAGON

cgplab/PAMES

Tool to estimate purity of tumor samples exploiting DNA Methylation data

LieberInstitute/Alzheimers_DNAm

Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls

NGSchoolEU/ngs17

Materials used during #NGSchool2017

fuxialexander/marvel

Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape

fungenomics/HGG-oncohistones

Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)

bhardwaj-lab/sincei

A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data

guanjue/IDEAS_2018

Jointly characterizing epigenetic dynamics across multiple cell types

johnlcd/CIRCScan

Toolkit for circRNA prediction by machine learning

GabrielHoffman/decorate

Differential Epigenetic Correlation Test

gifford-lab/deepaccess-package

Methods for training and interpretation of an ensemble of neural networks for multi-task functional prediction of accessibility or histone modifications from DNA sequence.

omics-datascience/multiomix

Multiomix platform source code

rnajena/magnipore

Magnipore: Differential single nucleotide changes of ONT signals

salbrec/SIMPA