:dart: ChIP peak Annotation, Comparison and Visualization

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

Multiome GRN inference.

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

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

Methods for summarizing and visualizing multi-biosample functional genomic annotations

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Toolkit for single-cell DNA methylation analysis.

Python package to analyze DNA methylation data

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

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

Bead-based single-cell atac processing

Predicting regulatory DNA elements based on epigenomic signatures

Molecular interactions inference from single-cell multi-omics data

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

Application for semi-automated genomic annotation.

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

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

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

ChromSCape

Base-conversion Sequencing Aligner

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

No description provided.

Tool to estimate purity of tumor samples exploiting DNA Methylation data

Materials used during #NGSchool2017

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

Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape

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)

Multiomix platform source code

Jointly characterizing epigenetic dynamics across multiple cell types